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
3.0.0 (Updated)
Bug Fixes
Documentation
- update documentaion (215aa2a)