Release notes v0.15.1

Same release notes as for v0.15.0 but with new cnv_sv module.

Coverage and mutations for ENC

The coverage and mutations file for ENC have been modified, with added hotspots and removal of PTEN.

CNV caller Jumble

The CNV caller Jumble has been added and the results are reporterd in the tsv and html reports.

CNV HTML / TSV report

Cytobands added
MUC6 region removed from VAF-plot as it was noisy
CDH1 gene is not reported anymore (CHD1 was the correct gene which is reported)
FP-flag added that flags probable false CNV calls made by CNVkit by looking at the data points in that region for GATK CNV.
BAF-limits of tsv-report increased to decrease number of reported copy neutral lohs (0.4=>0.3, 0.6=>0.7)

MultiQC

Pipeline version is now in the report
MultiQC version updated which introduced some nessesary changes:
Use samtools stats to report number of aligned reads instead of picard
Insert size standard deviation removed

RNA fusion filter

Added the RPSAP52:HMGA2 fusion as it has been showing up in many samples
Added the posibility to filter certain fusion by allele frequency

Sample mixup

The DNA / RNA sample mixup test cutoff is now configurable and decreased as default to 0.7. Changed bcftools caller to -c to slighly increase the genotype concordance betwwen RNA and DNA in cases with lots of CNVs.

Bugfixes

Rare case of of bug in the RNA-fusion report has been fixed, where it crashed when FusionCatcher did not able to liftover breakpoint positions to HG19.
The version report could make the pipeline crash when the pipeline run over to the next day. Date is now avoided in the file path.
Handle non-called ID-SNP correctly (due to low coverage)

Changes in config.yaml

cnv_html_report:
  cytobands: true
  
cnv_tsv_report:
  amp_chr_arm_cn_limit: 2.6
  normal_baf_lower_limit: 0.3
  normal_baf_upper_limit: 0.7
  max_cnv_fp_size: 15000000
  
jumble_cnvkit_call:
  container: "docker://hydragenetics/cnvkit:0.9.9"

jumble_run:
  container: "docker://hydragenetics/jumble:240530"

jumble_vcf:
  dup_limit: 2.5
  het_del_limit: 1.5
  hom_del_limit: 0.5
  
merge_cnv_json:
  filtered_cnv_vcfs:
    - cnv_sv/svdb_query/{sample}_{type}.{tc_method}.svdb_query.annotate_cnv.cnv_amp_genes.filter.cnv_hard_filter_amp.fp_tag.vcf
    - cnv_sv/svdb_query/{sample}_{type}.{tc_method}.svdb_query.annotate_cnv.cnv_loh_genes_all.filter.cnv_hard_filter_loh.fp_tag.annotate_fp.vcf
  germline_vcf: snv_indels/bcbio_variation_recall_ensemble/{sample}_{type}.ensembled.vep_annotated.filter.germline.exclude.blacklist.vcf.gz
  unfiltered_cnv_vcfs:
    - cnv_sv/svdb_query/{sample}_{type}.{tc_method}.svdb_query.annotate_cnv.cnv_amp_genes.fp_tag.vcf.gz
    - cnv_sv/svdb_query/{sample}_{type}.{tc_method}.svdb_query.annotate_cnv.cnv_loh_genes_all.fp_tag.vcf.gz
  unfiltered_cnv_vcfs_tbi:
    - cnv_sv/svdb_query/{sample}_{type}.{tc_method}.svdb_query.annotate_cnv.cnv_amp_genes.fp_tag.vcf.gz.tbi
    - cnv_sv/svdb_query/{sample}_{type}.{tc_method}.svdb_query.annotate_cnv.cnv_loh_genes_all.fp_tag.vcf.gz.tbi
    
multiqc:
  container: "docker://hydragenetics/multiqc:1.21"
  reports:
    DNA_umi:
      config: "config/reports/multiqc_config_dna.yaml"
      
sample_mixup_check:
  match_cutoff: 0.7
  
svdb_merge:
  container: "docker://hydragenetics/svdb:2.6.0"
  tc_method:
    - name: pathology_purecn
      cnv_caller:
        - cnvkit
        - gatk
        - jumble
      priority: "cnvkit,gatk,jumble"
    - name: purecn
      cnv_caller:
        - cnvkit
        - gatk
        - jumble
      priority: "cnvkit,gatk,jumble"
    - name: pathology
      cnv_caller:
        - cnvkit
        - gatk
        - jumble
      priority: "cnvkit,gatk,jumble"

Changes in config.data.hg19.yaml

annotate_cnv:
  cnv_loh_genes_all: "{{PROJECT_DESIGN_DATA}}/GMS560/cnv/cnv_loh_genes_240618.bed"
  
bcftools_filter_exclude_region:
  blacklist: "{{PROJECT_DESIGN_DATA}}/GMS560/cnv/cnvkit_germline_blacklist_20240613.bed"

call_small_cnv_deletions:
  regions_file: "{{PROJECT_DESIGN_DATA}}/GMS560/cnv/cnv_deletion_genes_240618.tsv"
  
hotspot_report:
  hotspot_mutations: 
    ENC: "{{PROJECT_DESIGN_DATA}}/GMS560/reports/ENC_hotspots_240919.csv"

jumble_run:
  normal_reference: "{{PROJECT_DESIGN_DATA}}/GMS560/cnv/jumble/jumble.combined.filtered.50.PoN.hg19.RDS"
  
merge_cnv_json:
  cytobands: "{{PROJECT_DESIGN_DATA}}/GMS560/cnv/cytoBand.hg19.txt"
  
report_fusions:
  fp_fusions: "{{PROJECT_DESIGN_DATA}}/GMS560/rna_fusion/filter_rna_fusions_20240923.txt"

Changes in config_references.yaml

jumble_count:
  container: "docker://hydragenetics/jumble:240530"

jumble_reference:
  container: "docker://hydragenetics/jumble:240530"
  annotation: "/projects/wp1/nobackup/ngs/utveckling/Twist_DNA_DATA/jumble/jumble_annotation/"

Changes in resources

jumble_run:
  threads: 10

Hydra modules with releases

prealignment: v1.0.0 (No change)
alignment: v0.5.0 (No change)
snv_indels: v0.3.0 (No change)
annotation: v1.1.0 (Updated)
filtering: v0.3.0 (No change)
qc: v0.5.0 (Updated)
biomarker: v0.4.0 (No change)
fusions: v0.1.0 (No change)
cnv_sv: v0.7.1 (Updated)
reports: v0.5.0 (Updated)
misc: removed

Snakemake min version

7.18.0 (no change)

Hydra genetics min version

3.0.0 (Updated)

Hydra genetics common singularity version