diff --git a/.test_data/data/0.01x_3_wgs_HG002_hg38.samplesheet.csv b/.test_data/data/0.01x_3_wgs_HG002_hg38.samplesheet.csv
index 918882f..94d4dd3 100755
--- a/.test_data/data/0.01x_3_wgs_HG002_hg38.samplesheet.csv
+++ b/.test_data/data/0.01x_3_wgs_HG002_hg38.samplesheet.csv
@@ -1,4 +1,4 @@
 samp,sample,sample_lane,SQ,RU,EX,LANE,r1_path,r2_path,biological_sex,iddna_uid,concordance_control_path,is_positive_control,is_negative_control,sample_type,merge_single,tum_nrm_sampleid_match,external_sample_id,instrument,lib_prep,bwa_kmer,subsample_pct
-RIH0_ANA0-HG002_DBC0_0,RIH0_ANA0-HG002_DBC0_0,RIH0_ANA0-HG002_DBC0_0,DBC0,RIH0,ANA0-HG002,0,.test_data/data/RIH0_ANA0-HG002_DBC0_0.R1.fastq.gz,.test_data/data/RIH0_ANA0-HG002_DBC0_0.R2.fastq.gz,male,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG2/,true,false,blood,merge,HG002,HG002,NOVASEQ,PCR-FREE,19,0.95
-RIH0_ANA0-HG002_DBC1_0,RIH0_ANA0-HG002_DBC1_2,RIH0_ANA0-HG002_DBC1_2,DBC2,RIH0,ANA0-HG002,2,.test_data/data/RIH0_ANA0-HG002_DBC0_0.R1.fastq.gz,.test_data/data/RIH0_ANA0-HG002_DBC0_0.R2.fastq.gz,male,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG2/,true,false,blood,merge,HG002,HG002,NOVASEQ,PCR-FREE,19,0.85
-RIH0_ANA0-HG002_DBC1_0,RIH0_ANA0-HG002_DBC1_1,RIH0_ANA0-HG002_DBC1_1,DBC1,RIH0,ANA0-HG002,1,.test_data/data/RIH0_ANA0-HG002_DBC0_0.R1.fastq.gz,.test_data/data/RIH0_ANA0-HG002_DBC0_0.R2.fastq.gz,male,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG2/,true,false,blood,merge,HG002,HG002,NOVASEQ,PCR-FREE,19,0.75
+RIH0_ANA0-HG002_DBC0_0,RIH0_ANA0-HG002_DBC0_0,RIH0_ANA0-HG002_DBC0_0,DBC0,RIH0,ANA0-HG002,0,.test_data/data/RIH0_ANA0-HG002_DBC0_0.R1.fastq.gz,.test_data/data/RIH0_ANA0-HG002_DBC0_0.R2.fastq.gz,male,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG2/,true,false,blood,merge,na,HG002,NOVASEQ,PCR-FREE,19,0.95
+RIH0_ANA0-HG002_DBC1_0,RIH0_ANA0-HG002_DBC1_2,RIH0_ANA0-HG002_DBC1_2,DBC2,RIH0,ANA0-HG002,2,.test_data/data/RIH0_ANA0-HG002_DBC0_0.R1.fastq.gz,.test_data/data/RIH0_ANA0-HG002_DBC0_0.R2.fastq.gz,male,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG2/,true,false,blood,merge,na,HG002,NOVASEQ,PCR-FREE,19,0.85
+RIH0_ANA0-HG002_DBC1_0,RIH0_ANA0-HG002_DBC1_1,RIH0_ANA0-HG002_DBC1_1,DBC1,RIH0,ANA0-HG002,1,.test_data/data/RIH0_ANA0-HG002_DBC0_0.R1.fastq.gz,.test_data/data/RIH0_ANA0-HG002_DBC0_0.R2.fastq.gz,male,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG2/,true,false,blood,na,HG002,HG002,NOVASEQ,PCR-FREE,19,0.75
diff --git a/.test_data/data/0.01xwgs_HG002_b37.samplesheet.csv b/.test_data/data/0.01xwgs_HG002_b37.samplesheet.csv
index 72ba6c3..a65cb87 100755
--- a/.test_data/data/0.01xwgs_HG002_b37.samplesheet.csv
+++ b/.test_data/data/0.01xwgs_HG002_b37.samplesheet.csv
@@ -1,2 +1,2 @@
 samp,sample,sample_lane,SQ,RU,EX,LANE,r1_path,r2_path,biological_sex,iddna_uid,concordance_control_path,is_positive_control,is_negative_control,sample_type,merge_single,tum_nrm_sampleid_match,external_sample_id,instrument,lib_prep,bwa_kmer
-RIH0_ANA0-HG002_DBC0_0,RIH0_ANA0-HG002_DBC0_0,RIH0_ANA0-HG002_DBC0_0,DBC0,RIH0,ANA0-HG002,0,.test_data/data/RIH0_ANA0-HG002_DBC0_0.R1.fastq.gz,.test_data/data/RIH0_ANA0-HG002_DBC0_0.R2.fastq.gz,male,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/b37/controls/giab/snv/v4.2.1/HG002/,true,false,blood,merge,HG002,HG002,NOVASEQ,PCR-FREE,19
+RIH0_ANA0-HG002_DBC0_0,RIH0_ANA0-HG002_DBC0_0,RIH0_ANA0-HG002_DBC0_0,DBC0,RIH0,ANA0-HG002,0,.test_data/data/RIH0_ANA0-HG002_DBC0_0.R1.fastq.gz,.test_data/data/RIH0_ANA0-HG002_DBC0_0.R2.fastq.gz,male,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/b37/controls/giab/snv/v4.2.1/HG002/,true,false,blood,merge,na,HG002,NOVASEQ,PCR-FREE,19
diff --git a/.test_data/data/0.01xwgs_HG002_hg38.samplesheet.csv b/.test_data/data/0.01xwgs_HG002_hg38.samplesheet.csv
index d96d481..8399c88 100755
--- a/.test_data/data/0.01xwgs_HG002_hg38.samplesheet.csv
+++ b/.test_data/data/0.01xwgs_HG002_hg38.samplesheet.csv
@@ -1,2 +1,2 @@
 samp,sample,sample_lane,SQ,RU,EX,LANE,r1_path,r2_path,biological_sex,iddna_uid,concordance_control_path,is_positive_control,is_negative_control,sample_type,merge_single,tum_nrm_sampleid_match,external_sample_id,instrument,lib_prep,bwa_kmer
-RIH0_ANA0-HG002_DBC0_0,RIH0_ANA0-HG002_DBC0_0,RIH0_ANA0-HG002_DBC0_0,DBC0,RIH0,ANA0-HG002,0,.test_data/data/RIH0_ANA0-HG002_DBC0_0.R1.fastq.gz,.test_data/data/RIH0_ANA0-HG002_DBC0_0.R2.fastq.gz,male,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG2/,true,false,blood,merge,HG002,HG002,NOVASEQ,PCR-FREE,19
+RIH0_ANA0-HG002_DBC0_0,RIH0_ANA0-HG002_DBC0_0,RIH0_ANA0-HG002_DBC0_0,DBC0,RIH0,ANA0-HG002,0,.test_data/data/RIH0_ANA0-HG002_DBC0_0.R1.fastq.gz,.test_data/data/RIH0_ANA0-HG002_DBC0_0.R2.fastq.gz,male,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG2/,true,false,blood,merge,na,HG002,NOVASEQ,PCR-FREE,19
diff --git a/.test_data/data/giab_30x_b37_analysis_manifest.csv b/.test_data/data/giab_30x_b37_analysis_manifest.csv
index 62bb2b2..a5f9ec5 100755
--- a/.test_data/data/giab_30x_b37_analysis_manifest.csv
+++ b/.test_data/data/giab_30x_b37_analysis_manifest.csv
@@ -1,8 +1,8 @@
 samp,sample,sample_lane,SQ,RU,EX,LANE,r1_path,r2_path,biological_sex,iddna_uid,concordance_control_path,is_positive_control,is_negative_control,sample_type,merge_single,tum_nrm_sampleid_match,external_sample_id,instrument,lib_prep,bwa_kmer
-R0_HG001_D0_0,R0_HG001_D0_0,R0_HG001_D0_0,D0,R0,HG001,0,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG001_30x_R1.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG001_30x_R2.fastq.gz,female,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/b37/controls/giab/snv/v4.2.1/HG001/,true,false,blood,merge,HG001,HG001,NOVASEQ,PCR-FREE,19
-R0_HG002_D0_0,R0_HG002_D0_0,R0_HG002_D0_0,D0,R0,HG002,0,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG002_30x_R1.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG002_30x_R2.fastq.gz,male,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/b37/controls/giab/snv/v4.2.1/HG002/,true,false,blood,merge,HG002,HG002,NOVASEQ,PCR-FREE,19
-R0_HG003_D0_0,R0_HG003_D0_0,R0_HG003_D0_0,D0,R0,HG003,0,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG003_30x_R1.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG003_30x_R2.fastq.gz,male,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/b37/controls/giab/snv/v4.2.1/HG003/,true,false,blood,merge,HG003,HG003,NOVASEQ,PCR-FREE,19
-R0_HG004_D0_0,R0_HG004_D0_0,R0_HG004_D0_0,D0,R0,HG004,0,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG004_30x_R1.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG004_30x_R2.fastq.gz,female,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/b37/controls/giab/snv/v4.2.1/HG004/,true,false,blood,merge,HG004,HG004,NOVASEQ,PCR-FREE,19
-R0_HG005_D0_0,R0_HG005_D0_0,R0_HG005_D0_0,D0,R0,HG005,0,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG005_30x_R1.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG005_30x_R2.fastq.gz,male,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/b37/controls/giab/snv/v4.2.1/HG005/,true,false,blood,merge,HG005,HG005,NOVASEQ,PCR-FREE,19
-R0_HG006_D0_0,R0_HG006_D0_0,R0_HG006_D0_0,D0,R0,HG006,0,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG006_30x_R1.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG006_30x_R2.fastq.gz,male,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/b37/controls/giab/snv/v4.2.1/HG006/,true,false,blood,merge,HG006,HG006,NOVASEQ,PCR-FREE,19
-R0_HG007_D0_0,R0_HG007_D0_0,R0_HG007_D0_0,D0,R0,HG007,0,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG007_30x_R1.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG007_30x_R2.fastq.gz,female,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/b37/controls/giab/snv/v4.2.1/HG007/,true,false,blood,merge,HG007,HG007,NOVASEQ,PCR-FREE,19
+R0_HG001_D0_0,R0_HG001_D0_0,R0_HG001_D0_0,D0,R0,HG001,0,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG001_30x_R1.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG001_30x_R2.fastq.gz,female,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/b37/controls/giab/snv/v4.2.1/HG001/,true,false,blood,merge,na,HG001,NOVASEQ,PCR-FREE,19
+R0_HG002_D0_0,R0_HG002_D0_0,R0_HG002_D0_0,D0,R0,HG002,0,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG002_30x_R1.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG002_30x_R2.fastq.gz,male,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/b37/controls/giab/snv/v4.2.1/HG002/,true,false,blood,merge,na,HG002,NOVASEQ,PCR-FREE,19
+R0_HG003_D0_0,R0_HG003_D0_0,R0_HG003_D0_0,D0,R0,HG003,0,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG003_30x_R1.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG003_30x_R2.fastq.gz,male,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/b37/controls/giab/snv/v4.2.1/HG003/,true,false,blood,merge,na,HG003,NOVASEQ,PCR-FREE,19
+R0_HG004_D0_0,R0_HG004_D0_0,R0_HG004_D0_0,D0,R0,HG004,0,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG004_30x_R1.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG004_30x_R2.fastq.gz,female,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/b37/controls/giab/snv/v4.2.1/HG004/,true,false,blood,merge,na,HG004,NOVASEQ,PCR-FREE,19
+R0_HG005_D0_0,R0_HG005_D0_0,R0_HG005_D0_0,D0,R0,HG005,0,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG005_30x_R1.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG005_30x_R2.fastq.gz,male,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/b37/controls/giab/snv/v4.2.1/HG005/,true,false,blood,merge,na,HG005,NOVASEQ,PCR-FREE,19
+R0_HG006_D0_0,R0_HG006_D0_0,R0_HG006_D0_0,D0,R0,HG006,0,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG006_30x_R1.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG006_30x_R2.fastq.gz,male,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/b37/controls/giab/snv/v4.2.1/HG006/,true,false,blood,merge,na,HG006,NOVASEQ,PCR-FREE,19
+R0_HG007_D0_0,R0_HG007_D0_0,R0_HG007_D0_0,D0,R0,HG007,0,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG007_30x_R1.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG007_30x_R2.fastq.gz,female,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/b37/controls/giab/snv/v4.2.1/HG007/,true,false,blood,merge,na,HG007,NOVASEQ,PCR-FREE,19
diff --git a/.test_data/data/giab_30x_hg38_analysis_manifest.csv b/.test_data/data/giab_30x_hg38_analysis_manifest.csv
index ddf4b7c..f2a41ce 100755
--- a/.test_data/data/giab_30x_hg38_analysis_manifest.csv
+++ b/.test_data/data/giab_30x_hg38_analysis_manifest.csv
@@ -1,8 +1,8 @@
 samp,sample,sample_lane,SQ,RU,EX,LANE,r1_path,r2_path,biological_sex,iddna_uid,concordance_control_path,is_positive_control,is_negative_control,sample_type,merge_single,tum_nrm_sampleid_match,external_sample_id,instrument,lib_prep,bwa_kmer
-R0_HG001_D0_0,R0_HG001_D0_0,R0_HG001_D0_0,D0,R0,HG001,0,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG001_30x_R1.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG001_30x_R2.fastq.gz,female,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG001/,true,false,blood,merge,HG001,HG001,NOVASEQ,PCR-FREE,19
-R0_HG002_D0_0,R0_HG002_D0_0,R0_HG002_D0_0,D0,R0,HG002,0,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG002_30x_R1.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG002_30x_R2.fastq.gz,male,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG002/,true,false,blood,merge,HG002,HG002,NOVASEQ,PCR-FREE,19
-R0_HG003_D0_0,R0_HG003_D0_0,R0_HG003_D0_0,D0,R0,HG003,0,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG003_30x_R1.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG003_30x_R2.fastq.gz,male,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG003/,true,false,blood,merge,HG003,HG003,NOVASEQ,PCR-FREE,19
-R0_HG004_D0_0,R0_HG004_D0_0,R0_HG004_D0_0,D0,R0,HG004,0,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG004_30x_R1.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG004_30x_R2.fastq.gz,female,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG004/,true,false,blood,merge,HG004,HG004,NOVASEQ,PCR-FREE,19
-R0_HG005_D0_0,R0_HG005_D0_0,R0_HG005_D0_0,D0,R0,HG005,0,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG005_30x_R1.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG005_30x_R2.fastq.gz,male,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG005/,true,false,blood,merge,HG005,HG005,NOVASEQ,PCR-FREE,19
-R0_HG006_D0_0,R0_HG006_D0_0,R0_HG006_D0_0,D0,R0,HG006,0,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG006_30x_R1.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG006_30x_R2.fastq.gz,male,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG006/,true,false,blood,merge,HG006,HG006,NOVASEQ,PCR-FREE,19
-R0_HG007_D0_0,R0_HG007_D0_0,R0_HG007_D0_0,D0,R0,HG007,0,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG007_30x_R1.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG007_30x_R2.fastq.gz,female,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG007/,true,false,blood,merge,HG007,HG007,NOVASEQ,PCR-FREE,19
+R0_HG001_D0_0,R0_HG001_D0_0,R0_HG001_D0_0,D0,R0,HG001,0,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG001_30x_R1.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG001_30x_R2.fastq.gz,female,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG001/,true,false,blood,merge,na,HG001,NOVASEQ,PCR-FREE,19
+R0_HG002_D0_0,R0_HG002_D0_0,R0_HG002_D0_0,D0,R0,HG002,0,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG002_30x_R1.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG002_30x_R2.fastq.gz,male,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG002/,true,false,blood,merge,na,HG002,NOVASEQ,PCR-FREE,19
+R0_HG003_D0_0,R0_HG003_D0_0,R0_HG003_D0_0,D0,R0,HG003,0,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG003_30x_R1.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG003_30x_R2.fastq.gz,male,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG003/,true,false,blood,merge,na,HG003,NOVASEQ,PCR-FREE,19
+R0_HG004_D0_0,R0_HG004_D0_0,R0_HG004_D0_0,D0,R0,HG004,0,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG004_30x_R1.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG004_30x_R2.fastq.gz,female,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG004/,true,false,blood,merge,na,HG004,NOVASEQ,PCR-FREE,19
+R0_HG005_D0_0,R0_HG005_D0_0,R0_HG005_D0_0,D0,R0,HG005,0,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG005_30x_R1.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG005_30x_R2.fastq.gz,male,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG005/,true,false,blood,merge,na,HG005,NOVASEQ,PCR-FREE,19
+R0_HG006_D0_0,R0_HG006_D0_0,R0_HG006_D0_0,D0,R0,HG006,0,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG006_30x_R1.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG006_30x_R2.fastq.gz,male,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG006/,true,false,blood,merge,na,HG006,NOVASEQ,PCR-FREE,19
+R0_HG007_D0_0,R0_HG007_D0_0,R0_HG007_D0_0,D0,R0,HG007,0,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG007_30x_R1.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG007_30x_R2.fastq.gz,female,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG007/,true,false,blood,merge,na,HG007,NOVASEQ,PCR-FREE,19
diff --git a/config/day_profiles/local/templates/rule_config.yaml b/config/day_profiles/local/templates/rule_config.yaml
index 1b8979c..4da46f2 100755
--- a/config/day_profiles/local/templates/rule_config.yaml
+++ b/config/day_profiles/local/templates/rule_config.yaml
@@ -15,7 +15,7 @@ valid_biome: AWSPC
 
 # ###### Tool Selection CONFIG ----------------------------------------
 
-# these may be set on the command line as --config genome_build=hg38 aligners=['bwa2a','sent','strobe']  dedupers=['dppl']  snv_callers=['oct','clair3','deep','sentd','lfq2'] sv_callers=['manta','tiddit','dysgu']
+# these may be set on the command line as --config genome_build=hg38 aligners=['bwa2a','sent','strobe']  dedupers=['dppl']  snv_callers=['oct','clair3','deep','sentd','lfq2','strelka2'] sv_callers=['manta','tiddit','dysgu']
 # and will override these defaults
 
 # Or you can set them here
@@ -196,6 +196,7 @@ deepsomatic:
     numa: " OMP_NUM_THREADS=8 OMP_PROC_BIND=close OMP_PLACES=threads OMP_PROC_BIND=TRUE OMP_DYNAMIC=TRUE OMP_MAX_ACTIVE_LEVELS=1 OMP_SCHEDULE=dynamic OMP_WAIT_POLICY=ACTIVE "
     dvsom_conda: "../envs/vanilla_v0.1.yaml"
 
+
 mutect2:
     threads: 7
     container: "docker://broadinstitute/gatk:4.5.0.0"
@@ -208,6 +209,7 @@ mutect2:
     numa: ""
     conda: "../envs/vanilla_v0.1.yaml"
 
+
 duphold:
     threads: 7
     env_yaml: "../envs/duphold_v0.1.yaml"
diff --git a/config/day_profiles/slurm/templates/rule_config.yaml b/config/day_profiles/slurm/templates/rule_config.yaml
index 65ce5da..3d0e471 100755
--- a/config/day_profiles/slurm/templates/rule_config.yaml
+++ b/config/day_profiles/slurm/templates/rule_config.yaml
@@ -14,7 +14,7 @@ valid_biome: AWSPC
 
 # ###### Tool Selection CONFIG ----------------------------------------
 
-# these may be set on the command line as --config genome_build=hg38 aligners=['bwa2a','sent','strobe']  dedupers=['dppl']  snv_callers=['oct','clair3','deep','sentd','lfq2'] sv_callers=['manta','tiddit','dysgu']
+# these may be set on the command line as --config genome_build=hg38 aligners=['bwa2a','sent','strobe']  dedupers=['dppl']  snv_callers=['oct','clair3','deep','sentd','lfq2','strelka2'] sv_callers=['manta','tiddit','dysgu']
 
 # and will override these defaults
 
@@ -209,6 +209,7 @@ mutect2:
 
 
 
+
 duphold:
     threads: 32
     env_yaml: "../envs/duphold_v0.1.yaml"
diff --git a/giab_30x_hg38_analysis_manifest.csv b/giab_30x_hg38_analysis_manifest.csv
old mode 100755
new mode 100644
index e8ad19d..62b3ed6
--- a/giab_30x_hg38_analysis_manifest.csv
+++ b/giab_30x_hg38_analysis_manifest.csv
@@ -1,9 +1,9 @@
-samp,sample,sample_lane,SQ,RU,EX,LANE,r1_path,r2_path,biological_sex,iddna_uid,concordance_control_path,is_positive_control,is_negative_control,sample_type,merge_single,tum_nrm_sampleid_match,external_sample_id,instrument,lib_prep,bwa_kmer
-R0_HG001_D0_0,R0_HG001_D0_0,R0_HG001_D0_0,D0,R0,HG001,0,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG001_30x_R1.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG001_30x_R2.fastq.gz,female,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG001/,true,false,blood,merge,HG001,HG001,NOVASEQ,PCR-FREE,19
-R0_HG002_D0_0,R0_HG002_D0_0,R0_HG002_D0_0,D0,R0,HG002,0,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG002_30x_R1.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG002_30x_R2.fastq.gz,male,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG002/,true,false,blood,merge,HG002,HG002,NOVASEQ,PCR-FREE,19
-R0_HG003_D0_0,R0_HG003_D0_0,R0_HG003_D0_0,D0,R0,HG003,0,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG003_30x_R1.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG003_30x_R2.fastq.gz,male,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG003/,true,false,blood,merge,HG003,HG003,NOVASEQ,PCR-FREE,19
-R0_HG004_D0_0,R0_HG004_D0_0,R0_HG004_D0_0,D0,R0,HG004,0,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG004_30x_R1.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG004_30x_R2.fastq.gz,female,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG004/,true,false,blood,merge,HG004,HG004,NOVASEQ,PCR-FREE,19
-R0_HG005_D0_0,R0_HG005_D0_0,R0_HG005_D0_0,D0,R0,HG005,0,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG005_30x_R1.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG005_30x_R2.fastq.gz,male,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG005/,true,false,blood,merge,HG005,HG005,NOVASEQ,PCR-FREE,19
-R0_HG006_D0_0,R0_HG006_D0_0,R0_HG006_D0_0,D0,R0,HG006,0,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG006_30x_R1.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG006_30x_R2.fastq.gz,male,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG006/,true,false,blood,merge,HG006,HG006,NOVASEQ,PCR-FREE,19
-R0_HG007_D0_0,R0_HG007_D0_0,R0_HG007_D0_0,D0,R0,HG007,0,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG007_30x_R1.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG007_30x_R2.fastq.gz,female,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG007/,true,false,blood,merge,HG007,HG007,NOVASEQ,PCR-FREE,19
+SQ,RU,EX,LANE,r1_path,r2_path,biological_sex,iddna_uid,concordance_control_path,is_positive_control,is_negative_control,sample_type,merge_single,tum_nrm_sampleid_match,external_sample_id,instrument,lib_prep,bwa_kmer
+D0,R0,HG001,0,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG001_30x_R1.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG001_30x_R2.fastq.gz,female,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG001/,true,false,blood,merge,HG001,HG001,NOVASEQ,PCR-FREE,19
+D0,R0,HG002,0,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG002_30x_R1.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG002_30x_R2.fastq.gz,male,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG002/,true,false,blood,merge,HG002,HG002,NOVASEQ,PCR-FREE,19
+D0,R0,HG003,0,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG003_30x_R1.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG003_30x_R2.fastq.gz,male,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG003/,true,false,blood,merge,HG003,HG003,NOVASEQ,PCR-FREE,19
+D0,R0,HG004,0,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG004_30x_R1.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG004_30x_R2.fastq.gz,female,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG004/,true,false,blood,merge,HG004,HG004,NOVASEQ,PCR-FREE,19
+D0,R0,HG005,0,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG005_30x_R1.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG005_30x_R2.fastq.gz,male,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG005/,true,false,blood,merge,HG005,HG005,NOVASEQ,PCR-FREE,19
+D0,R0,HG006,0,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG006_30x_R1.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG006_30x_R2.fastq.gz,male,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG006/,true,false,blood,merge,HG006,HG006,NOVASEQ,PCR-FREE,19
+D0,R0,HG007,0,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG007_30x_R1.fastq.gz,/fsx/data/genomic_data/organism_reads/H_sapiens/giab/NovaSeqX_WHGS_TruSeqPF_HG002-007/HG007_30x_R2.fastq.gz,female,na,/fsx/data/genomic_data/organism_annotations/H_sapiens/hg38/controls/giab/snv/v4.2.1/HG007/,true,false,blood,merge,HG007,HG007,NOVASEQ,PCR-FREE,19
 
diff --git a/workflow/envs/vpot_v0.1.yaml b/workflow/envs/vpot_v0.1.yaml
index e456502..378e504 100644
--- a/workflow/envs/vpot_v0.1.yaml
+++ b/workflow/envs/vpot_v0.1.yaml
@@ -1,11 +1,7 @@
 channels:
   - conda-forge
   - bioconda
-  - anaconda
-  - r
-  - defaults
 dependencies:
-  - python
+  - python=3.9
+  - numpy
   - pip
-  - pip:
-      - git+https://github.com/VCCRI/VPOT.git
diff --git a/workflow/rules/mutect2.smk b/workflow/rules/mutect2.smk
index 50736d2..44b76fc 100644
--- a/workflow/rules/mutect2.smk
+++ b/workflow/rules/mutect2.smk
@@ -38,89 +38,88 @@ rule mutect2_bams:
         r"""
         set -euo pipefail
         ulimit -n 65536 || true
-        
-        mkdir -p "$(dirname {output.tumor_bam}"
+
+        mkdir -p "$(dirname {output.tumor_bam})"
 
         # Build interval token; map 23→X, 24→Y, 25→{params.mito_code}; strip trailing colon.
         tchr=$(echo {params.cpre}{params.chrm} \
         | sed 's/~/\:/g' | sed 's/23\:/X\:/' | sed 's/24\:/Y\:/' | sed 's/25\:/{params.mito_code}\:/')
-        tchr=${{tchr}}
+        tchr=${{tchr%:}}
 
         IFS=':' read -r tcontig tstart tend <<< "$tchr"
 
         # Look up contig length early
         contig_len=$(awk -v c="$tcontig" '$1==c{{print $2; exit}}' {input.ref_fai})
         if [ -z "${{contig_len}}" ]; then
-          echo "ERROR: Contig '$tcontig' not found in {input.ref_fai}" >&2
-          exit 1
+        echo "ERROR: Contig '$tcontig' not found in {input.ref_fai}" >&2
+        exit 1
         fi
 
-        if [ -z "${{tend}}" ]; then
-          # Whole contig
-          region="$tcontig"
+        if [ -z "${{tend:-}}" ]; then
+        # Whole contig
+        region="$tcontig"
         else
-          # Normalize to 1-based inclusive and clamp to [1, contig_len]
-          if [ -z "${{tstart}}" ] || [ "$tstart" -lt 1 ]; then tstart=1; fi
-          if [ "$tend" -gt "$contig_len" ]; then tend="$contig_len"; fi
-          if [ "$tstart" -gt "$tend" ]; then
+        # Normalize to 1-based inclusive and clamp to [1, contig_len]
+        : "${{tstart:=1}}"
+        if [ "$tstart" -lt 1 ]; then tstart=1; fi
+        if [ "$tend" -gt "$contig_len" ]; then tend="$contig_len"; fi
+        if [ "$tstart" -gt "$tend" ]; then
             echo "ERROR: Empty/invalid interval after normalization: $tcontig:$tstart-$tend" >&2
             exit 1
-          fi
-          region="$tcontig:$tstart-$tend"
         fi
-        
+        region="$tcontig:$tstart-$tend"
+        fi
+
         # Tumor
         samtools view -@ {threads} -T {input.ref_fa} -b {input.tumor_cram} "$region" \
-          | samtools sort -@ {threads} -o {output.tumor_bam} -           >> {log} 2>&1
-        samtools index -@ {threads} {output.tumor_bam}                    >> {log} 2>&1
-        
+        | samtools sort -@ {threads} -o {output.tumor_bam} -                >> {log} 2>&1
+        samtools index -@ {threads} {output.tumor_bam}                         >> {log} 2>&1
+
         # Normal
         samtools view -@ {threads} -T {input.ref_fa} -b {input.normal_cram} "$region" \
-          | samtools sort -@ {threads} -o {output.normal_bam} -          >> {log} 2>&1
-        samtools index -@ {threads} {output.normal_bam}                   >> {log} 2>&1
-
+        | samtools sort -@ {threads} -o {output.normal_bam} -               >> {log} 2>&1
+        samtools index -@ {threads} {output.normal_bam}                        >> {log} 2>&1
 
-        # ---- Fix SM in headers (preserve all other @RG fields) ----
+        # ---- Fix SM in headers (preserve other @RG fields) ----
         fix_sm () {{
-          inbam=$1
-          outbam=$2
-          sm=$3
-          tmphdr=$(mktemp)
-          OFS="\t"
-          samtools view -H "$inbam" \
-            | awk -v sm="$sm" 'BEGIN{OFS="\t"}
-                /^@RG/ {
-                  hasSM=0
-                  for (i=1;i<=NF;i++){
-                    if ($i ~ /^SM:/) { $i="SM:" sm; hasSM=1 }
-                  }
-                  if (!hasSM){ $0 = $0 OFS "SM:" sm }
-                }
-                { print }
-              ' > "$tmphdr"
-          # Reheader and replace atomically
-          samtools reheader "$tmphdr" "$inbam" > "$outbam"
-          rm -f "$tmphdr"
-          samtools index -@ {threads} "$outbam" >/dev/null 2>&1 || true
+        inbam=$1
+        outbam=$2
+        sm=$3
+        tmphdr=$(mktemp)
+        samtools view -H "$inbam" \
+            | awk -v sm="$sm" 'BEGIN{{FS=OFS="\t"}}
+                /^@RG/ {{
+                found=0
+                for (i=1;i<=NF;i++) if ($i ~ /^SM:/) {{ $i="SM:" sm; found=1 }}
+                if (!found) {{ $0 = $0 OFS "SM:" sm }}
+                }}
+                {{ print }}
+            ' > "$tmphdr"
+        samtools reheader "$tmphdr" "$inbam" > "$outbam"
+        rm -f "$tmphdr"
+        samtools index -@ {threads} "$outbam" >/dev/null 2>&1 || true
         }}
-        
-        # Distinct names for tumor/normal (required by Mutect2)
-        T_SM="{params.cluster_sample}-T"
-        N_SM="{params.cluster_sample}-N"
-        
+
+        tum_sample=$(echo "{input.tumor_cram}" | sed -E 's#.*/([^/]+)/align/.*#\1#')
+        nrm_sample=$(echo "{input.normal_cram}" | sed -E 's#.*/([^/]+)/align/.*#\1#')
+
+        echo "Tumor Sample: $tum_sample"   >> {log} 2>&1
+        echo "Normal Sample: $nrm_sample"  >> {log} 2>&1
+        T_SM="${{tum_sample}}"
+        N_SM="${{nrm_sample}}"
+
+
         fix_sm "{output.tumor_bam}"  "{output.tumor_bam}.smfix" "$T_SM"
         mv "{output.tumor_bam}.smfix" "{output.tumor_bam}"
-        samtools index -@ {threads} -f "{output.tumor_bam}"                     >> {log} 2>&1
-        
+        samtools index -@ {threads}  "{output.tumor_bam}"                    >> {log} 2>&1
+
         fix_sm "{output.normal_bam}" "{output.normal_bam}.smfix" "$N_SM"
         mv "{output.normal_bam}.smfix" "{output.normal_bam}"
-        samtools index -@ {threads} -f "{output.normal_bam}"                    >> {log} 2>&1
-        
-        # Optional: log the final names for sanity  
-        gatk GetSampleName -I {output.tumor_bam} 2>>{log} | sed "s/^/Tumor SM: /"  >> {log}
-        gatk GetSampleName -I {output.normal_bam} 2>>{log} | sed "s/^/Normal SM: /" >> {log}
+        samtools index -@ {threads} "{output.normal_bam}"                   >> {log} 2>&1
+
         """
 
+
 rule mutect2:
     wildcard_constraints:
         sample=TUMORS_REGEX
diff --git a/workflow/rules/rule_common.smk b/workflow/rules/rule_common.smk
index 4b9ea9b..8540a5b 100755
--- a/workflow/rules/rule_common.smk
+++ b/workflow/rules/rule_common.smk
@@ -92,6 +92,7 @@ LOFREQ_CHRMS = config["lofreq2"][f"{config['genome_build']}_lofreq_chrms"].split
 DVSOM_CHRMS = config["deepsomatic"][f"{config['genome_build']}_dvsom_chrms"].split(",")
 M2_CHRMS = config["mutect2"][f"{config['genome_build']}_mutect2_chrms"].split(",")
 SENTTN_CHRMS = config["senttn"][f"{config['genome_build']}_senttn_chrms"].split(",")
+STRELKA2_CHRMS = config["strelka2"][f"{config['genome_build']}_strelka2_chrms"].split(",")
 
 VARN_CHRMS = (
     []
@@ -242,9 +243,36 @@ os.system(
 )
 
 # IMPORTANT: initialize the samples dataframe from the analysis_manifest.csv
-samples = pd.read_table(analysis_manifest, ",").set_index(
-    ["sample", "sample_lane"], drop=False
-)
+samples = pd.read_table(analysis_manifest, ",")
+
+# Derive sample_lane and sample identifiers if they are not provided.
+required_cols = {"RU", "EX", "SQ", "LANE"}
+missing = required_cols - set(samples.columns)
+if missing:
+    raise WorkflowError(f"Missing required columns in analysis manifest: {missing}")
+
+samples["LANE"] = samples["LANE"].astype(int)
+
+if "sample_lane" not in samples.columns:
+    samples["sample_lane"] = (
+        samples["RU"].astype(str)
+        + "_"
+        + samples["EX"].astype(str)
+        + "_"
+        + samples["SQ"].astype(str)
+        + "_"
+        + samples["LANE"].astype(str)
+    )
+
+if "sample" not in samples.columns:
+    samples["sample"] = samples.apply(
+        lambda r: f"{r['RU']}_{r['EX']}_{r['SQ']}_0"
+        if str(r.get("merge_single", "")).lower() == "merge"
+        else r["sample_lane"],
+        axis=1,
+    )
+
+samples = samples.set_index(["sample", "sample_lane"], drop=False)
 
 # Ensure tum_nrm_sampleid_match exists and treat missing values as 'na'
 if "tum_nrm_sampleid_match" in samples.columns:
@@ -953,6 +981,7 @@ def get_mutect2_chrm_day(wildcards):
 
     if len(sl2) == 2:
         ret_str = pchr + wildcards.m2chrm
+
     elif len(sl) == 1:
         ret_str = pchr + sl[0]
     elif len(sl) == 2:
@@ -964,6 +993,7 @@ def get_mutect2_chrm_day(wildcards):
     else:
         raise Exception(
             "mutect2 chunks can only be one contiguous range per chunk : ie: 1-4 with the non numerical chrms assigned 23=X, 24=Y,25=MT"
+
         )
 
     return ret_mod_chrm(ret_str)
diff --git a/workflow/rules/strelka2.smk b/workflow/rules/strelka2.smk
new file mode 100644
index 0000000..b2cdfc7
--- /dev/null
+++ b/workflow/rules/strelka2.smk
@@ -0,0 +1,295 @@
+import sys
+import os
+
+##### strelka2
+# ---------------------------
+
+rule strelka2_germline_chunkdirs:
+    input:
+        b=MDIR + "{sample}/align/{alnr}/{sample}.{alnr}.cram",
+        i=MDIR + "{sample}/align/{alnr}/{sample}.{alnr}.cram.crai",
+    output:
+        expand(
+            MDIR + "{{sample}}/align/{{alnr}}/snv/slk2g/vcfs/{strelkachrm}/{{sample}}.ready",
+            strelkachrm=STRELKA2_CHRMS,
+        ),
+    threads: 1
+    log:
+        MDIR + "{sample}/align/{alnr}/snv/slk2g/log/{sample}.{alnr}.chunkdirs.log",
+    shell:
+        """
+        ( echo {output}; mkdir -p $(dirname {output}); touch {output}; ls {output}; ) > {log} 2>&1;
+        """
+
+
+rule strelka2_germline:
+    input:
+        cram=MDIR + "{sample}/align/{alnr}/{sample}.{alnr}.cram",
+        crai=MDIR + "{sample}/align/{alnr}/{sample}.{alnr}.cram.crai",
+        ref_fa=lambda wc: config["supporting_files"]["files"]["huref"]["fasta"]["name"],
+        d=MDIR + "{sample}/align/{alnr}/snv/slk2g/vcfs/{strelkachrm}/{sample}.ready",
+    output:
+        vcfgz=MDIR + "{sample}/align/{alnr}/snv/slk2g/vcfs/{strelkachrm}/{sample}.{alnr}.strelka2.{strelkachrm}.germline.vcf.gz",
+        vcftbi=MDIR + "{sample}/align/{alnr}/snv/slk2g/vcfs/{strelkachrm}/{sample}.{alnr}.strelka2.{strelkachrm}.germline.vcf.gz.tbi",
+    log:
+        MDIR + "{sample}/align/{alnr}/snv/slk2g/vcfs/{strelkachrm}/log/{sample}.{alnr}.strelka2.{strelkachrm}.germline.log",
+    threads: config['strelka2']['threads']
+    container:
+        config['strelka2']['container']
+    resources:
+        vcpu=config['strelka2']['threads'],
+        threads=config['strelka2']['threads'],
+        partition=config['strelka2']['partition'],
+        mem_mb=config['strelka2']['mem_mb'],
+    params:
+        run_dir=MDIR + "{sample}/align/{alnr}/snv/slk2g/work/{sample}.germline.{strelkachrm}",
+        schrm=get_strelka_chrm_day,
+        cluster_sample=ret_sample,
+        cpre="" if "b37" == config['genome_build'] else "chr",
+        mito_code="MT" if "b37" == config['genome_build'] else "M",
+    shell:
+        r"""
+        set -euo pipefail
+        mkdir -p {params.run_dir}
+
+        vchr=$(echo {params.cpre}{params.schrm} | sed 's/~/\:/g' | sed 's/23\:/X\:/' | sed 's/24\:/Y\:/' | sed 's/25\:/{params.mito_code}\:/' )
+        vchr=${{vchr%:}}
+        IFS=':' read -r vcontig vstart vend <<< "$vchr"
+        if [ -z "${{vend:-}}" ]; then
+            vstart=0
+            vend=$(awk -v c="$vcontig" '$1==c{{print $2; exit}}' {input.ref_fa}.fai)
+        fi
+        echo -e "$vcontig\t$vstart\t$vend" > {params.run_dir}/region.bed
+
+        configureStrelkaGermlineWorkflow.py \
+            --bam {input.cram} \
+            --referenceFasta {input.ref_fa} \
+            --callRegions {params.run_dir}/region.bed \
+            --runDir {params.run_dir} >> {log} 2>&1
+        {params.run_dir}/runWorkflow.py -m local -j {threads} >> {log} 2>&1
+        cp {params.run_dir}/results/variants/variants.vcf.gz {output.vcfgz}
+        cp {params.run_dir}/results/variants/variants.vcf.gz.tbi {output.vcftbi}
+        """
+
+
+rule strelka2_germline_concat:
+    input:
+        vcfs=lambda wildcards: expand(
+            MDIR + "{sample}/align/{alnr}/snv/slk2g/vcfs/{strelkachrm}/{sample}.{alnr}.strelka2.{strelkachrm}.germline.vcf.gz",
+            sample=wildcards.sample,
+            alnr=wildcards.alnr,
+            strelkachrm=STRELKA2_CHRMS,
+        ),
+    output:
+        vcfgz=MDIR + "{sample}/align/{alnr}/snv/slk2g/{sample}.{alnr}.strelka2.germline.vcf.gz",
+        vcfgztbi=MDIR + "{sample}/align/{alnr}/snv/slk2g/{sample}.{alnr}.strelka2.germline.vcf.gz.tbi",
+    threads: 4
+    resources:
+        vcpu=4,
+        threads=4,
+        partition=config['strelka2']['partition'],
+        mem_mb=config['strelka2']['mem_mb'],
+    conda: "../envs/vanilla_v0.1.yaml"
+    log:
+        MDIR + "{sample}/align/{alnr}/snv/slk2g/log/{sample}.{alnr}.strelka2.germline.merge.log",
+    params:
+        cluster_sample=ret_sample,
+    shell:
+        """
+        bcftools concat -a -d all --threads {threads} -O z -o {output.vcfgz}.tmp {input.vcfs} >> {log} 2>&1;
+        oldname=$(bcftools query -l {output.vcfgz}.tmp | head -n1) >> {log} 2>&1;
+        echo -e "${{oldname}}\t{params.cluster_sample}" > {output.vcfgz}.rename.txt;
+        bcftools reheader -s {output.vcfgz}.rename.txt -o {output.vcfgz} {output.vcfgz}.tmp >> {log} 2>&1;
+        bcftools index -f -t --threads {threads} {output.vcfgz} >> {log} 2>&1;
+        rm -f {output.vcfgz}.tmp {output.vcfgz}.rename.txt;
+        """
+
+
+rule strelka2_somatic_chunkdirs:
+    wildcard_constraints:
+        sample=TUMORS_REGEX
+    input:
+        b=MDIR + "{sample}/align/{alnr}/{sample}.{alnr}.cram",
+        i=MDIR + "{sample}/align/{alnr}/{sample}.{alnr}.cram.crai",
+    output:
+        expand(
+            MDIR + "{{sample}}/align/{{alnr}}/snv/slk2s/vcfs/{strelkachrm}/{{sample}}.ready",
+            strelkachrm=STRELKA2_CHRMS,
+        ),
+    threads: 1
+    log:
+        MDIR + "{sample}/align/{alnr}/snv/slk2s/log/{sample}.{alnr}.somatic.chunkdirs.log",
+    shell:
+        """
+        ( echo {output}; mkdir -p $(dirname {output}); touch {output}; ls {output}; ) > {log} 2>&1;
+        """
+
+
+rule strelka2_somatic:
+    wildcard_constraints:
+        sample=TUMORS_REGEX
+    input:
+        tumor_cram=get_somcall_tumor_cram,
+        tumor_crai=get_somcall_tumor_crai,
+        normal_cram=get_somcall_normal_cram,
+        normal_crai=get_somcall_normal_crai,
+        ref_fa=lambda wc: config["supporting_files"]["files"]["huref"]["fasta"]["name"],
+        d=MDIR + "{sample}/align/{alnr}/snv/slk2s/vcfs/{strelkachrm}/{sample}.ready",
+    output:
+        snv=MDIR + "{sample}/align/{alnr}/snv/slk2s/vcfs/{strelkachrm}/{sample}.{alnr}.strelka2.{strelkachrm}.somatic.snvs.vcf.gz",
+        snvtbi=MDIR + "{sample}/align/{alnr}/snv/slk2s/vcfs/{strelkachrm}/{sample}.{alnr}.strelka2.{strelkachrm}.somatic.snvs.vcf.gz.tbi",
+        indel=MDIR + "{sample}/align/{alnr}/snv/slk2s/vcfs/{strelkachrm}/{sample}.{alnr}.strelka2.{strelkachrm}.somatic.indels.vcf.gz",
+        indeltbi=MDIR + "{sample}/align/{alnr}/snv/slk2s/vcfs/{strelkachrm}/{sample}.{alnr}.strelka2.{strelkachrm}.somatic.indels.vcf.gz.tbi",
+    log:
+        MDIR + "{sample}/align/{alnr}/snv/slk2s/vcfs/{strelkachrm}/log/{sample}.{alnr}.strelka2.{strelkachrm}.somatic.log",
+    threads: config['strelka2']['threads']
+    container:
+        config['strelka2']['container']
+    resources:
+        vcpu=config['strelka2']['threads'],
+        threads=config['strelka2']['threads'],
+        partition=config['strelka2']['partition'],
+        mem_mb=config['strelka2']['mem_mb'],
+    params:
+        run_dir=MDIR + "{sample}/align/{alnr}/snv/slk2s/work/{sample}.somatic.{strelkachrm}",
+        schrm=get_strelka_chrm_day,
+        cluster_sample=ret_sample,
+        cpre="" if "b37" == config['genome_build'] else "chr",
+        mito_code="MT" if "b37" == config['genome_build'] else "M",
+    shell:
+        r"""
+        set -euo pipefail
+        mkdir -p {params.run_dir}
+
+        vchr=$(echo {params.cpre}{params.schrm} | sed 's/~/\:/g' | sed 's/23\:/X\:/' | sed 's/24\:/Y\:/' | sed 's/25\:/{params.mito_code}\:/' )
+        vchr=${{vchr%:}}
+        IFS=':' read -r vcontig vstart vend <<< "$vchr"
+        if [ -z "${{vend:-}}" ]; then
+            vstart=0
+            vend=$(awk -v c="$vcontig" '$1==c{{print $2; exit}}' {input.ref_fa}.fai)
+        fi
+        echo -e "$vcontig\t$vstart\t$vend" > {params.run_dir}/region.bed
+
+        configureStrelkaSomaticWorkflow.py \
+            --tumorBam {input.tumor_cram} \
+            --normalBam {input.normal_cram} \
+            --referenceFasta {input.ref_fa} \
+            --callRegions {params.run_dir}/region.bed \
+            --runDir {params.run_dir} >> {log} 2>&1
+        {params.run_dir}/runWorkflow.py -m local -j {threads} >> {log} 2>&1
+        cp {params.run_dir}/results/variants/somatic.snvs.vcf.gz {output.snv}
+        cp {params.run_dir}/results/variants/somatic.snvs.vcf.gz.tbi {output.snvtbi}
+        cp {params.run_dir}/results/variants/somatic.indels.vcf.gz {output.indel}
+        cp {params.run_dir}/results/variants/somatic.indels.vcf.gz.tbi {output.indeltbi}
+        """
+
+
+rule strelka2_somatic_concat:
+    wildcard_constraints:
+        sample=TUMORS_REGEX
+    input:
+        snv_vcfs=lambda wildcards: expand(
+            MDIR + "{sample}/align/{alnr}/snv/slk2s/vcfs/{strelkachrm}/{sample}.{alnr}.strelka2.{strelkachrm}.somatic.snvs.vcf.gz",
+            sample=wildcards.sample,
+            alnr=wildcards.alnr,
+            strelkachrm=STRELKA2_CHRMS,
+        ),
+        indel_vcfs=lambda wildcards: expand(
+            MDIR + "{sample}/align/{alnr}/snv/slk2s/vcfs/{strelkachrm}/{sample}.{alnr}.strelka2.{strelkachrm}.somatic.indels.vcf.gz",
+            sample=wildcards.sample,
+            alnr=wildcards.alnr,
+            strelkachrm=STRELKA2_CHRMS,
+        ),
+    output:
+        snv=MDIR + "{sample}/align/{alnr}/snv/slk2s/{sample}.{alnr}.strelka2.somatic.snvs.vcf.gz",
+        snvtbi=MDIR + "{sample}/align/{alnr}/snv/slk2s/{sample}.{alnr}.strelka2.somatic.snvs.vcf.gz.tbi",
+        indel=MDIR + "{sample}/align/{alnr}/snv/slk2s/{sample}.{alnr}.strelka2.somatic.indels.vcf.gz",
+        indeltbi=MDIR + "{sample}/align/{alnr}/snv/slk2s/{sample}.{alnr}.strelka2.somatic.indels.vcf.gz.tbi",
+    threads: 4
+    resources:
+        vcpu=4,
+        threads=4,
+        partition=config['strelka2']['partition'],
+        mem_mb=config['strelka2']['mem_mb'],
+    conda: "../envs/vanilla_v0.1.yaml"
+    log:
+        MDIR + "{sample}/align/{alnr}/snv/slk2s/log/{sample}.{alnr}.strelka2.somatic.merge.log",
+    params:
+        cluster_sample=ret_sample,
+    shell:
+        """
+        bcftools concat -a -d all --threads {threads} -O z -o {output.snv}.tmp {input.snv_vcfs} >> {log} 2>&1;
+        oldname=$(bcftools query -l {output.snv}.tmp | head -n1) >> {log} 2>&1;
+        echo -e "${{oldname}}\t{params.cluster_sample}" > {output.snv}.rename.txt;
+        bcftools reheader -s {output.snv}.rename.txt -o {output.snv} {output.snv}.tmp >> {log} 2>&1;
+        bcftools index -f -t --threads {threads} {output.snv} >> {log} 2>&1;
+        rm -f {output.snv}.tmp {output.snv}.rename.txt;
+
+        bcftools concat -a -d all --threads {threads} -O z -o {output.indel}.tmp {input.indel_vcfs} >> {log} 2>&1;
+        oldname=$(bcftools query -l {output.indel}.tmp | head -n1) >> {log} 2>&1;
+        echo -e "${{oldname}}\t{params.cluster_sample}" > {output.indel}.rename.txt;
+        bcftools reheader -s {output.indel}.rename.txt -o {output.indel} {output.indel}.tmp >> {log} 2>&1;
+        bcftools index -f -t --threads {threads} {output.indel} >> {log} 2>&1;
+        rm -f {output.indel}.tmp {output.indel}.rename.txt;
+        """
+
+rule produce_strelka2_germline_vcf:
+    input:
+        vcftb=expand(
+            MDIR + "{sample}/align/{alnr}/snv/slk2g/{sample}.{alnr}.strelka2.germline.vcf.gz",
+            sample=SSAMPS,
+            alnr=ALIGNERS,
+        ),
+        vcftbi=expand(
+            MDIR + "{sample}/align/{alnr}/snv/slk2g/{sample}.{alnr}.strelka2.germline.vcf.gz.tbi",
+            sample=SSAMPS,
+            alnr=ALIGNERS,
+        ),
+    output:
+        "gatheredall.strelka2.germline",
+    threads: 4
+    log:
+        "gatheredall.strelka2.germline.log",
+    params:
+        cluster_sample=ret_sample,
+    resources:
+        vcpu=4,
+        threads=4,
+        partition=config['strelka2']['partition'],
+        mem_mb=config['strelka2']['mem_mb'],
+
+
+rule produce_strelka2_somatic_vcf:
+    input:
+        snv=expand(
+            MDIR + "{sample}/align/{alnr}/snv/slk2s/{sample}.{alnr}.strelka2.somatic.snvs.vcf.gz",
+            sample=TN_TUMOR_SAMPS,
+            alnr=ALIGNERS,
+        ),
+        snvtbi=expand(
+            MDIR + "{sample}/align/{alnr}/snv/slk2s/{sample}.{alnr}.strelka2.somatic.snvs.vcf.gz.tbi",
+            sample=TN_TUMOR_SAMPS,
+            alnr=ALIGNERS,
+        ),
+        indel=expand(
+            MDIR + "{sample}/align/{alnr}/snv/slk2s/{sample}.{alnr}.strelka2.somatic.indels.vcf.gz",
+            sample=TN_TUMOR_SAMPS,
+            alnr=ALIGNERS,
+        ),
+        indeltbi=expand(
+            MDIR + "{sample}/align/{alnr}/snv/slk2s/{sample}.{alnr}.strelka2.somatic.indels.vcf.gz.tbi",
+            sample=TN_TUMOR_SAMPS,
+            alnr=ALIGNERS,
+        ),
+    output:
+        "gatheredall.strelka2.somatic",
+    threads: 4
+    log:
+        "gatheredall.strelka2.somatic.log",
+    params:
+        cluster_sample=ret_sample,
+    resources:
+        vcpu=4,
+        threads=4,
+        partition=config['strelka2']['partition'],
+        mem_mb=config['strelka2']['mem_mb'],
diff --git a/workflow/schemas/analysis_manifest.schema.yaml b/workflow/schemas/analysis_manifest.schema.yaml
index 6e2cfd9..b9c234d 100755
--- a/workflow/schemas/analysis_manifest.schema.yaml
+++ b/workflow/schemas/analysis_manifest.schema.yaml
@@ -5,10 +5,16 @@ description: Analysis Samples Manifest Validator.  See README in config section
 properties:
     sample:
         type: string
-        description: format RU#_EX_SQ#_LANE where LANE leading zeros removed, and if merged lane =0
+        description: >
+            Combination of RU, EX, SQ and lane used internally by the
+            workflow. If omitted, it will be generated automatically from
+            other fields.
     sample_lane:
         type: string
-        description: RU#_EX_SQ#_LANE with no lane substitution. Identifes the sub patterns to merge to create sample if merging is enabled.  if merge_single=single then sample==sample_lane. if merge, then sample_lane is unique, sample is the aggregation pattern, which may be 1 to 1, but if set to merge should be 1(sample) pattern to >1(sample_lane) patterns.<--- this was implemented, then scaled back, and now is largely only really working for merging.
+        description: >
+            Fully qualified sample identifier including lane. When not
+            provided, it will be derived automatically from RU, EX, SQ and
+            LANE.
     SQ:
         type: string
         description: Sample Type
@@ -58,8 +64,6 @@ properties:
     ont_cram_snv_caller:
         type: string
 required:
-    - sample
-    - sample_lane
     - SQ
     - RU
     - EX