Twist_Solid v0.18.3

Release notes v0.18.1, v0.18.2 and v0.18.3

Fixes

v0.18.3 fixes a bug in the cnv html report where some calls could be missing. The logic in the reported variants was updated to handle three callers correctly.
v0.18.3 also removes the extra line in the MultiQC report.

Three notemp fixes: general report input file that were missing as it is only specified in a config and optitype temp directory that removed all output. Also, all temporary files from purecn was removed to avoid checkpoint issues that came up in the v0.18.1.

Features

v0.18.3 introduces the possibility to change the tumor content in the cnv html report.

Release notes v0.18.0

Features

MSI site filtering

Now calculates both filtered and unfiltered MSI scores. The filtered sites are approximately 400 sites chosen to be informative MSI sites reducing noise and enabling us to better differenciate MSI from MSS in Endometrial cancer (ENC)

New fusion caller (JuLI)

Performs similar or better than FuseqWES. Good complement as it finds some new true fusions. Also has a shorter wall-time.

General result report

A general result report for each samples is added where results are collected and links are supplied to various results files in addition to smaple specific QC data.

HLA typing

Added HLA typing of HLA-A, HLA-B, and HLA-C with 4 digit resolution (ie HLA-A*02:01).

Save germline vcf

The germilne vaf could be useful to save in case of for example contamination

Fixes

Correct NA handling of Jumble calls

Jumble does not report BAF values which caused problems in the filtering used in the reports of CNVs. This caused lots of neutral copy variant to pass the filtering. Now missing values return True and the filtering works as expected.

MultiQC DNA

The general table had several lines per sample. This will be fixed in next release.

Reference pipeline: MSI Panel of normal

Corrected the generation of the MSI PoN so that all the steps are run and not only the scan for MSI sites.

Changes in config.yaml

general_report: "config/reports/general_report.yaml"

general_html_report:
  final_directory_depth: 4
  multiqc_config: "config/reports/multiqc_config_dna.yaml"

juli_annotate:
  container: "docker://hydragenetics/juli:0.1.6.2"

juli_call:
  container: "docker://hydragenetics/juli:0.1.6.2"

optitype:
  container: "docker://fred2/optitype:release-v1.3.1"

Changes in config/config.data.hg19.yaml

juli_annotate:
  cosmic: "{{PROJECT_REF_DATA}}/ref_data/juli/CosmicFusionExport_V76.tsv"
  pfam: "{{PROJECT_REF_DATA}}/ref_data/juli/Pfam-A.full.human"
  ref_genes: "{{PROJECT_REF_DATA}}/ref_data/juli/refGene_hg19.txt"
  uniprot: "{{PROJECT_REF_DATA}}/ref_data/juli/HGNC_GeneName_UniProtID_160524.txt"

juli_call:
  gap_file: "{{PROJECT_REF_DATA}}/ref_data/juli/gap_hg19.txt"
  ref_genes: "{{PROJECT_REF_DATA}}/ref_data/juli/refGene_hg19.txt"
  
msisensor_pro: 
=>
msisensor_pro_filter_sites:
  PoN: "{{PROJECT_PON_DATA}}/GMS560/PoN/Msisensor_pro_reference_nextseq_36.list_baseline"
  msi_sites_bed: "{{PROJECT_PON_DATA}}/GMS560/design/SelectedMSIloci2019Sorted.bed"

Hydra modules with releases

• prealignment: v1.0.0 (No change)
• alignment: v0.5.0 (No change)
• snv_indels: v1.1.0 (No change)
• annotation: v1.1.0 (No change)
• filtering: v0.3.0 (No change)
• qc: v0.5.0 (No change)
• biomarker: v0.5.0 (MSI filtering)
• fusions: v0.2.2 (JuLI fusion calling)
• cnv_sv: v0.7.0 (No change)
• reports: v0.7.0 (Adds General results report and TC in cnv_html_report)

Snakemake min version

7.18.0 (no change)

Hydra genetics min version

3.0.0 (no change)

Hydra genetics common singularity version

3.0.0 (no change)

Bug Fixes

• broken links (34d15fe)
• Snakefile: Fix linting (97f4acf)
• Snakefile: Linting (d36806e)
• Snakefile: Linting again... (a2ddc3c)
• Snakefile: Linting... (b7b3954)
• Snakefile: No temporary files in purecn out (a4f662c)
• hla: Correct results folder structure for HLA calling files (ad73f94)
• one row per sample in MultiQC report (9feab74)
• rm fp from html report (1265f46)
• update html-report to latest merge-cnv with table bugfix (5e89b41)
• update style to latest report version (66bfad2)
• update to latest report module (9afee9c)

Twist_Solid v0.18.2

Release notes v0.18.1 and v0.18.2

Fixes

Three notemp fixes: general report input file that were missing as it is only specified in a config and optiype temp directory that removed all output. Also, all temporary files from purecn was removed to avoid checkpoint issues that came up in the v0.18.1.

Release notes v0.18.0

Features

MSI site filtering

Now calculates both filtered and unfiltered MSI scores. The filtered sites are approximately 400 sites chosen to be informative MSI sites reducing noise and enabling us to better differenciate MSI from MSS in Endometrial cancer (ENC)

New fusion caller (JuLI)

Performs similar or better than FuseqWES. Good complement as it finds some new true fusions. Also has a shorter wall-time.

General result report

A general result report for each samples is added where results are collected and links are supplied to various results files in addition to smaple specific QC data.

HLA typing

Added HLA typing of HLA-A, HLA-B, and HLA-C with 4 digit resolution (ie HLA-A*02:01).

Save germline vcf

The germilne vaf could be useful to save in case of for example contamination

Fixes

Correct NA handling of Jumble calls

Jumble does not report BAF values which caused problems in the filtering used in the reports of CNVs. This caused lots of neutral copy variant to pass the filtering. Now missing values return True and the filtering works as expected.

MultiQC DNA

The general table had several lines per sample. This will be fixed in next release.

Reference pipeline: MSI Panel of normal

Corrected the generation of the MSI PoN so that all the steps are run and not only the scan for MSI sites.

Changes in config.yaml

general_report: "config/reports/general_report.yaml"

general_html_report:
  final_directory_depth: 4
  multiqc_config: "config/reports/multiqc_config_dna.yaml"

juli_annotate:
  container: "docker://hydragenetics/juli:0.1.6.2"

juli_call:
  container: "docker://hydragenetics/juli:0.1.6.2"

optitype:
  container: "docker://fred2/optitype:release-v1.3.1"

Changes in config/config.data.hg19.yaml

juli_annotate:
  cosmic: "{{PROJECT_REF_DATA}}/ref_data/juli/CosmicFusionExport_V76.tsv"
  pfam: "{{PROJECT_REF_DATA}}/ref_data/juli/Pfam-A.full.human"
  ref_genes: "{{PROJECT_REF_DATA}}/ref_data/juli/refGene_hg19.txt"
  uniprot: "{{PROJECT_REF_DATA}}/ref_data/juli/HGNC_GeneName_UniProtID_160524.txt"

juli_call:
  gap_file: "{{PROJECT_REF_DATA}}/ref_data/juli/gap_hg19.txt"
  ref_genes: "{{PROJECT_REF_DATA}}/ref_data/juli/refGene_hg19.txt"
  
msisensor_pro: 
=>
msisensor_pro_filter_sites:
  PoN: "{{PROJECT_PON_DATA}}/GMS560/PoN/Msisensor_pro_reference_nextseq_36.list_baseline"
  msi_sites_bed: "{{PROJECT_PON_DATA}}/GMS560/design/SelectedMSIloci2019Sorted.bed"

Hydra modules with releases

• prealignment: v1.0.0 (No change)
• alignment: v0.5.0 (No change)
• snv_indels: v1.1.0 (No change)
• annotation: v1.1.0 (No change)
• filtering: v0.3.0 (No change)
• qc: v0.5.0 (No change)
• biomarker: v0.5.0 (MSI filtering)
• fusions: v0.2.2 (JuLI fusion calling)
• cnv_sv: v0.7.0 (No change)
• reports: v0.6.0 (General results report)

Snakemake min version

7.18.0 (no change)

Hydra genetics min version

3.0.0 (no change)

Hydra genetics common singularity version

3.0.0 (no change)

Bug Fixes

• broken links (34d15fe)
• Snakefile: Fix linting (97f4acf)
• Snakefile: Linting (d36806e)
• Snakefile: Linting again... (a2ddc3c)
• Snakefile: Linting... (b7b3954)
• Snakefile: No temporary files in purecn out (a4f662c)

Twist_Solid v0.18.1

Release notes v0.18.1

Fixes

Two notemp fixes: general report input file that were missing as it is only specified in a config and optiype temp directory that removed all output.

Release notes v0.18.0

Features

MSI site filtering

Now calculates both filtered and unfiltered MSI scores. The filtered sites are approximately 400 sites chosen to be informative MSI sites reducing noise and enabling us to better differenciate MSI from MSS in Endometrial cancer (ENC)

New fusion caller (JuLI)

Performs similar or better than FuseqWES. Good complement as it finds some new true fusions. Also has a shorter wall-time.

General result report

A general result report for each samples is added where results are collected and links are supplied to various results files in addition to smaple specific QC data.

HLA typing

Added HLA typing of HLA-A, HLA-B, and HLA-C with 4 digit resolution (ie HLA-A*02:01).

Save germline vcf

The germilne vaf could be useful to save in case of for example contamination

Fixes

Correct NA handling of Jumble calls

Jumble does not report BAF values which caused problems in the filtering used in the reports of CNVs. This caused lots of neutral copy variant to pass the filtering. Now missing values return True and the filtering works as expected.

MultiQC DNA

The general table had several lines per sample. This is now fixed.

Reference pipeline: MSI Panel of normal

Corrected the generation of the MSI PoN so that all the steps are run and not only the scan for MSI sites.

Changes in config.yaml

general_report: "config/reports/general_report.yaml"

general_html_report:
  final_directory_depth: 4
  multiqc_config: "config/reports/multiqc_config_dna.yaml"

juli_annotate:
  container: "docker://hydragenetics/juli:0.1.6.2"

juli_call:
  container: "docker://hydragenetics/juli:0.1.6.2"

optitype:
  container: "docker://fred2/optitype:release-v1.3.1"

Changes in config/config.data.hg19.yaml

juli_annotate:
  cosmic: "{{PROJECT_REF_DATA}}/ref_data/juli/CosmicFusionExport_V76.tsv"
  pfam: "{{PROJECT_REF_DATA}}/ref_data/juli/Pfam-A.full.human"
  ref_genes: "{{PROJECT_REF_DATA}}/ref_data/juli/refGene_hg19.txt"
  uniprot: "{{PROJECT_REF_DATA}}/ref_data/juli/HGNC_GeneName_UniProtID_160524.txt"

juli_call:
  gap_file: "{{PROJECT_REF_DATA}}/ref_data/juli/gap_hg19.txt"
  ref_genes: "{{PROJECT_REF_DATA}}/ref_data/juli/refGene_hg19.txt"
  
msisensor_pro: 
=>
msisensor_pro_filter_sites:
  PoN: "{{PROJECT_PON_DATA}}/GMS560/PoN/Msisensor_pro_reference_nextseq_36.list_baseline"
  msi_sites_bed: "{{PROJECT_PON_DATA}}/GMS560/design/SelectedMSIloci2019Sorted.bed"

Hydra modules with releases

• prealignment: v1.0.0 (No change)
• alignment: v0.5.0 (No change)
• snv_indels: v1.1.0 (No change)
• annotation: v1.1.0 (No change)
• filtering: v0.3.0 (No change)
• qc: v0.5.0 (No change)
• biomarker: v0.5.0 (MSI filtering)
• fusions: v0.2.2 (JuLI fusion calling)
• cnv_sv: v0.7.0 (No change)
• reports: v0.6.0 (General results report)

Snakemake min version

7.18.0 (no change)

Hydra genetics min version

3.0.0 (no change)

Hydra genetics common singularity version

3.0.0 (no change)

Bug Fixes

• general report notemp issue (96e9da6)
• optitype: notemp issue (c362990)

Twist_Solid v0.18.0

Release notes v0.18.0

Features

MSI site filtering

Now calculates both filtered and unfiltered MSI scores. The filtered sites are approximately 400 sites chosen to be informative MSI sites reducing noise and enabling us to better differenciate MSI from MSS in Endometrial cancer (ENC)

New fusion caller (JuLI)

Performs similar or better than FuseqWES. Good complement as it finds some new true fusions. Also has a shorter wall-time.

General result report

A general result report for each samples is added where results are collected and links are supplied to various results files in addition to smaple specific QC data.

HLA typing

Added HLA typing of HLA-A, HLA-B, and HLA-C with 4 digit resolution (ie HLA-A*02:01).

Save germline vcf

The germilne vaf could be useful to save in case of for example contamination

Fixes

Correct NA handling of Jumble calls

Jumble does not report BAF values which caused problems in the filtering used in the reports of CNVs. This caused lots of neutral copy variant to pass the filtering. Now missing values return True and the filtering works as expected.

MultiQC DNA

The general table had several lines per sample. This is now fixed.

Reference pipeline: MSI Panel of normal

Corrected the generation of the MSI PoN so that all the steps are run and not only the scan for MSI sites.

Changes in config.yaml

general_report: "config/reports/general_report.yaml"

general_html_report:
  final_directory_depth: 4
  multiqc_config: "config/reports/multiqc_config_dna.yaml"

juli_annotate:
  container: "docker://hydragenetics/juli:0.1.6.2"

juli_call:
  container: "docker://hydragenetics/juli:0.1.6.2"

optitype:
  container: "docker://fred2/optitype:release-v1.3.1"

Changes in config/config.data.hg19.yaml

juli_annotate:
  cosmic: "{{PROJECT_REF_DATA}}/ref_data/juli/CosmicFusionExport_V76.tsv"
  pfam: "{{PROJECT_REF_DATA}}/ref_data/juli/Pfam-A.full.human"
  ref_genes: "{{PROJECT_REF_DATA}}/ref_data/juli/refGene_hg19.txt"
  uniprot: "{{PROJECT_REF_DATA}}/ref_data/juli/HGNC_GeneName_UniProtID_160524.txt"

juli_call:
  gap_file: "{{PROJECT_REF_DATA}}/ref_data/juli/gap_hg19.txt"
  ref_genes: "{{PROJECT_REF_DATA}}/ref_data/juli/refGene_hg19.txt"
  
msisensor_pro: 
=>
msisensor_pro_filter_sites:
  PoN: "{{PROJECT_PON_DATA}}/GMS560/PoN/Msisensor_pro_reference_nextseq_36.list_baseline"
  msi_sites_bed: "{{PROJECT_PON_DATA}}/GMS560/design/SelectedMSIloci2019Sorted.bed"

Hydra modules with releases

• prealignment: v1.0.0 (No change)
• alignment: v0.5.0 (No change)
• snv_indels: v1.1.0 (No change)
• annotation: v1.1.0 (No change)
• filtering: v0.3.0 (No change)
• qc: v0.5.0 (No change)
• biomarker: v0.5.0 (MSI filtering)
• fusions: v0.2.2 (JuLI fusion calling)
• cnv_sv: v0.7.0 (No change)
• reports: v0.6.0 (General results report)

Snakemake min version

7.18.0 (no change)

Hydra genetics min version

3.0.0 (no change)

Hydra genetics common singularity version

3.0.0 (no change)

Features

• add general report (ab3d9f4)
• add general report (28f0cef)
• msi: Calculate both filtered and unfiltered MSI score (e2f977a)
• msisensor_pro: add filtering of msi sites (d7e475e)
• save the germline vcf used in CNV analysis in results (368536d)

Bug Fixes

• add missing msisensor_pro override (c0b0db4)
• cnv_report: add missing cnv to report independent of number of callers (2bc9c2d)
• correct general report config (5404b87)
• correct general report config (661826d)
• correct MSIsensorpro output (cde79b6)
• correct reference path (dc36faf)
• est_input_develop.tsv: Space to tab (1428094)
• juli: update fusion module (d1cb1a6)
• jumble: NA-handling set to True for missing BAF values (e2731c2)
• missing config import (9e818c6)
• modify multiqc to define used output file (3b189e5)
• modify multiqc to define used output file (ffc4286)
• msi PoN override name correction (a89ba7f)
• msi: correct infiles to msi rules (8f4227f)
• msi: correct unfiltered msi output folder (cf97fc9)
• msisensor_pro: correct rule override (e9ec9c2)
• msi: spelling error (e5dac99)
• MultiQC: remove extra lines in MultiQC DNA report (b9c5dc1)
• references.hg19.yaml: JuLI ref-files (8415cb7)
• references.hg19.yaml: Removed citation mark (0c60ab5)
• rm extra line by hiding medium read length (42a4160)
• test_input_develop.tsv: Filtered/unfiltered msi (360f8f8)
• test_input_develop.tsv: New checksum msi_filtered (2567a84)
• test_input_develop.tsv: New sums for cnv-reports (3e4068b)
• test_input_develop.tsv: Spaces to tab (9da04d8)
• test_input_develop.tsv: Update sums (7293125)
• test_input_develop.tsv: Updated checksum (51a349a)
• test_input_main.tsv: New checksums (bda8469)
• test_input_main.tsv: Spaces to tabs (a37efd2)
• test_input_main.tsv: Update checksums (bbf1ed2)
• Update Snakefile (ee788a4)
• Update Snakefile_references.smk (5b8315b)
• vcf file should be gzipped (2b93e21)

Twist_Solid v0.17.0

Features

• Handling complex variants in snv_indel (73a003a)

Bug Fixes

• jumble: Update config.data.hg19.yaml (7b22ec5)
• jumble: Update config.data.hg38.yaml (6a8621d)
• sample_mixup: cut_off adjusted to percent (927e102)
• Snakefile_references: Wildcard_constrains, (5d48398)
• Snakefile: Added missing blank line. (f727111)
• Snakefile: Set wildcard_constraints cnv_sv (8639f34)
• Snakefile: Wildcard_constraints filter_vcf (2cca85f)
• Snakefile: zip and index qc-files (ba36799)
• test_input_develop.tsv: Updated checksums (4eadf6c)
• test_input_main.tsv: Update checksums (46ef91a)

Twist_Solid v0.16.0

Release notes v0.16.0

Only small fixes of the RNA pipeline and reference pipeline in comparison from v0.15.1

RNA pipeline

Fixed a division by zero error in the fusion report when coverage in region was unknown.
Removed extra lines per sample in the RNA MultiQC report and added the missing M aligned reads column.
The sample mixup report is now reported in percentage as it is written in the header.

Reference pipeline

Jumble PoN output name is dependent on the design file name. The output name in rule name is now automatically adjusted to what is set in the config file.
Cnvkit_batch input variables did not match that of the wrapper

Features

• make jumble reference name based on config (64db79b)

Bug Fixes

• add design wildcard to output (35e4514)
• cnvkit_batch: fix input variable name to match wrapper (996891d)
• design name as input to rule all (9c5d570)
• jumble output is dependent on design bed name (a4fd564)
• only use file name and not path (67c4be7)
• report_fusion: fix div by zero (68d253a)
• rm hardcoded jumble reference name (39e9d8f)
• rm multiple sample lines in MultiQC_RNA (94f445f)
• rm multiple sample lines in MultiQC_RNA (0470ecb)
• rm multiple sample lines in MultiQC_RNA (024ebcf)
• rm multiple sample lines in MultiQC_RNA (76f2cc8)
• sample mixup in percentage (733ac69)

Twist_Solid v0.15.1

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

• correction of output text for 1p19q (e98873b)
• update cnv_sv module (9c1f42d)

Documentation

• update documentaion (215aa2a)

Twist_Solid v0.15.0

Release notes v0.15.0

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: v0.7.0 (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)

Features

• adapt multiqc dna to new mmultiqc version (a46dfb7)
• add a rule which adds the FP_FLAG to vcf header (246f76a)
• add fp-flag column to html report (de38e72)
• add support for changing html report main table (954b90a)
• added cnv caller jumble (13918e2)
• added jumble reference to pipeline (4115c0c)
• added jumble to html report (a40021d)
• added jumble to html report (28a5403)
• added matck_cutoff to config (6405f2c)
• added new jumble PoN to reference files and configs (a986e9c)
• AF rna fusion filter possibility (d46e228)
• change calling model (36dd6aa)
• change max size for FP to 15M baser (0c10799)
• flag FP cnvkit dels and amps based on gatkcnv data (6ddbd02)
• make max size of cnv configurable (5fa5908)
• make sample_mixup_configurable (a0fdd26)
• make sample-mixup configurable (c6fbf03)
• rm CDH1 from reporting of cnv deletions (32cd1f5)
• rm noisy MUC6 from cnv VAF plot (a15663c)
• stricter BAF and cn criterias for chr aberations (9600785)
• update qc module to v0.5.0 to get correct samtools stats without bed file (71a3c0c)
• updated ENC hotspot files (3354710)
• updated multiqc for version info (71e8c8b)

Bug Fixes

• add '-' to FP-flag where missing (6e478f2)
• add FP_FLAG in header of all cnv vcf files (adeab23)
• add missing python module (8566c04)
• bu (ff962a4)
• bugfix (efa90d3)
• bugfix of version crash when...

Twist_Solid v0.14.0

Release notes v0.14.0

Panel of Normal for CNV:

New Panel of normal used as default for cnvkit that can be used for all sequencing machines as it combines normal samples from nextseq550, nextseq2000 and novaseq6000. There are still some issues with small FP deletions in some genes, like BRCA1.

Coverage and mutations:

The coverage for all positions marked as region_all are now reported. Before it was only positions with coverage below 300.
Added a second coverage and mutations file for ENC

UMI / Plamsa fusion calling

Use GeneFuse for fusion calling in plasma
Use relaxed filtering for FuseqWES (min 15 supporting reads). We also save the unfiltered outfile in results under additional files.

Changes in config.yaml

filter_fuseq_wes_umi:
  min_support: 15
  filter_on_fusiondb: True
  
gene_fuse:
  container: "docker://hydragenetics/genefuse:0.6.1"
  
report_gene_fuse:
  min_unique_reads: 6

Changes in config.data.hg19.yaml

cnvkit_batch:
  normal_reference: "{{PROJECT_PON_DATA}}/GMS560/PoN/cnvkit_PoN_combined_hg19.cnn"

filter_fuseq_wes_umi:
  gene_fusion_black_list: "{{PROJECT_DESIGN_DATA}}/GMS560/fuseq_wes/false_positive_fusion_pairs.txt"
  gene_white_list: "{{PROJECT_DESIGN_DATA}}/GMS560/fuseq_wes/fuseq_wes_gene_white_list.txt"
  transcript_black_list: "{{PROJECT_DESIGN_DATA}}/GMS560/fuseq_wes/fuseq_wes_transcript_black_list.txt"
  gtf: "{{PROJECT_REF_DATA}}/ref_data/refGene/hg19.refGene.gtf"

hotspot_report:
  chr_translation_file: "config/reports/hotspot_report.chr.translation.hg19"
  hotspot_mutations: 
    all: "{{PROJECT_DESIGN_DATA}}/GMS560/reports/Hotspots_combined_regions_nodups.231011.csv"
    ENC: "{{PROJECT_DESIGN_DATA}}/GMS560/reports/ENC_hotspots_240604.csv"

Changes in config.data.hg38.yaml

cnvkit_batch:
  normal_reference: "{{PROJECT_PON_DATA}}/GMS560/PoN/cnvkit_PoN_combined_hg38.cnn"

filter_fuseq_wes_umi:
  gene_fusion_black_list: "{{PROJECT_DESIGN_DATA}}/GMS560/fuseq_wes/false_positive_fusion_pairs.txt"
  gene_white_list: "{{PROJECT_DESIGN_DATA}}/GMS560/fuseq_wes/fuseq_wes_gene_white_list.txt"
  transcript_black_list: "{{PROJECT_DESIGN_DATA}}/GMS560/fuseq_wes/fuseq_wes_transcript_black_list.txt"
  gtf: "{{PROJECT_REF_DATA}}/ref_data/refGene/hg38.refGene.gtf"
  
gene_fuse:
  genes: "/projects/wp1/nobackup/ngs/utveckling/Twist_DNA_DATA/gene_fuse/GMS560_fusion_w_pool2.hg38.csv"
  fasta: "/data/ref_genomes/GRCh38_p14/homo_sapiens.fasta"
  
hotspot_report:
  chr_translation_file: "config/reports/hotspot_report.chr.translation.hg38"
  hotspot_mutations: 
    all: "{{PROJECT_DESIGN_DATA}}/GMS560/reports/Hotspots_combined_regions_nodups.231011_hg38.csv"
    ENC: "{{PROJECT_DESIGN_DATA}}/GMS560/reports/ENC_hotspots_240604_hg38.csv"

Changes in resources

None

Hydra modules with releases

• prealignment: v1.0.0 (No change)
• alignment: v0.5.0 (No change)
• snv_indels: v0.3.0 (No change)
• annotation: v1.0.1 (No change)
• filtering: v0.3.0 (No change)
• qc: v0.3.0 (No change)
• biomarker: v0.4.0 (No change)
• fusions: v0.1.0 (No change)
• cnv_sv: v0.3.1 (No change)
• reports: v0.4.1 (No change)
• misc: v0.2.0 (No change)

Snakemake min version

7.18.0 (no change)

Hydra genetics version

3.0.0 (Updated)

Hydra genetics common singularity version

3.0.0 (Updated)

Features

• add hotspot file for ENC (2de88ed)
• added blacklist filtering of small cnv deletions (f6e77bc)
• added ENC hotspot files for hg38 (0e06818)
• added separate filtering of fuseq wes for umi (8b83894)
• new PoN on figshare (41f3f0b)
• new PoN on figshare (f702d7c)
• new PoN on figshare hg38 (641e37d)
• reinstated genefuse for umi only (a5af752)
• update common container to new hydra (6f64d68)
• update hydra version (651c38f)
• use latestest version (365d3d2)
• use new PoN (e5bbd55)
• use new PoN hg38 (1151f3b)

Bug Fixes

• add missing singularity (24eeac6)
• added blacklist files to reference config (3450166)
• config schema (e727bd5)
• config schema (9470d56)
• correct reference files (4ff7a76)
• correct URL (ee7c8f6)
• corrected config (20fb88e)
• corrected novaseq hrd PoN download link (6ea893a)
• git version (4efd11f)
• git version (ef0891d)
• rm conda (210dfdc)
• update ENC hotspots (fec13d5)
• update ENC hotspots (8334f7a)
• update ENC hotspots (66dd017)
• update ENC hotspots (1338508)
• wrong release of design files (cc246f7)

Documentation

• added documentation (87fbda9)
• do not activate python env (8d28cdf)

Twist_Solid v0.13.0

Release notes v0.13.0

CNV html report

Large CNVs (> 30% of an chromosomal arm) are now reported in a new table in the html report.
There is a new warning in the new table when there are very few segments on the baseline suggesting that the baseline is shifted.
There is a new warning of polyploidy when there is large regions with BAF -signals that do not match with the copy numbers.

Two new genes reported for CNV amplifications.

The MDM2 gene as well as the C19MC miRNA cluster is now reported when amplications are found in these genes.

Changes in config.yaml

cnv_html_report:
  show_table: true
  show_cytobands: true
  extra_tables:
    - name: Small CNVs and 1p19q
      description: >
        Additional small amplifications and deletions as well as 1p19q co-deletions called by Twist Solid
        in-house scripts. Can have overlaps with called regions from other callers.
      path: "cnv_sv/svdb_query/{sample}_{type}.{tc_method}.cnv_loh_genes_all.cnv_additional_variants_only.tsv"
    - name: Large chromosomal aberrations
      description: >
        Large chromosomal aberrations in the form of deletions, duplications and copy neutral loss of heterozygosity.
        Also warnings of baseline skewness and detection of polyploidy in the sample.
      path: "cnv_sv/svdb_query/{sample}_{type}.{tc_method}.cnv_loh_genes_all.cnv_chromosome_arms.tsv"

cnv_tsv_report:
  amp_cn_limit: 6.0
  baseline_fraction_limit: 0.2
  del_1p19q_cn_limit: 1.4
  del_1p19q_chr_arm_fraction: 0.3
  chr_arm_fraction: 0.3
  del_chr_arm_cn_limit: 1.4
  amp_chr_arm_cn_limit: 2.5
  normal_baf_lower_limit: 0.4
  normal_baf_upper_limit: 0.6
  normal_cn_lower_limit: 1.7
  normal_cn_upper_limit: 2.25
  polyploidy_fraction_limit: 0.2

svdb_merge:
  container: "docker://hydragenetics/svdb:2.6.0"
  tc_method:
    - name: pathology_purecn
      cnv_caller:
        - cnvkit
        - gatk
    - name: purecn
      cnv_caller:
        - cnvkit
        - gatk
    - name: pathology
      cnv_caller:
        - cnvkit
        - gatk
  overlap: 1 #Just merge the two vcf-files without merging regions
  extra: "--pass_only" #Just merge the two vcf-files without merging regions

Changes in config.data.hg19.yaml

annotate_cnv:
  cnv_amp_genes: "{{PROJECT_DESIGN_DATA}}/GMS560/cnv/cnv_amp_genes_240307.bed"
  
call_small_cnv_amplifications:
  regions_file: "{{PROJECT_DESIGN_DATA}}/GMS560/cnv/cnv_amplification_genes_240307.tsv"
  
cnv_tsv_report:
  chrom_arm_size: "{{PROJECT_DESIGN_DATA}}/GMS560/cnv/chromosome_arm_size.tsv"

merge_cnv_json:
  annotations:
    - "{{PROJECT_DESIGN_DATA}}/GMS560/cnv/cnv_amp_genes_240307.bed"
    - "{{PROJECT_DESIGN_DATA}}/GMS560/cnv/cnv_loh_genes.bed"

Changes in config.data.hg38.yaml

Several file paths updated

Changes in resources

None

Hydra modules with releases

• prealignment: v1.0.0 (No change)
• alignment: v0.5.0 (No change)
• snv_indels: v0.3.0 (No change)
• annotation: v1.0.1 (No change)
• filtering: v0.3.0 (No change)
• qc: v0.3.0 (No change)
• biomarker: v0.4.0 (No change)
• fusions: v0.1.0 (No change)
• cnv_sv: v0.3.1 (No change)
• reports: v0.4.1 (No change)
• misc: v0.2.0 (No change)

Snakemake min version

7.18.0 (no change)

Hydra genetics version

1.14.0 (Updated)

Features

• added calculation of cnv in chrom arms (667d53f)
• added chromosome arm support to rule (ccbe735)
• added configuration of polyploidy and baseline limits (8f91b42)
• added more config variables (9a92bf2)
• added table to cnv_html_report (e577cdd)
• added warnings for baseline and polyploidy (9a25cdc)
• decreased chr arm fraction (b1ce417)
• do not merge regions that are not identical (1d9a027)
• new amp genes for hg38 (c6f7b5e)
• two new amplification genes reported (c8264b2)
• update ref files for hg38 (0ad022c)
• update test file for develop (36bab94)
• updated with new reference files (5e057e7)

Bug Fixes

• add "_" to regexp so that indels are reported correctly (7549036)
• add implied msi configuration from module to config (a9dea4e)
• bugfix (e681fee)
• correct missing part of vep ref file path (36b3b0a)
• handle CNVs bridging the chromosome arms (8a508ad)
• remove unused library that break requirements (86afc7d)
• rm duplicate entries of cnv in report (3a2cae4)
• spelling error (46aef96)
• update config, merge_cnv_json, to use latest amp gene bed file (be98e22)
• update hg38 ref files, point to correct release (e8efb8c)
• variable baf bugfix (d460172)

Documentation

• added config schemas for new params (62c832d)
• added schema (b1c9bfe)