From add06df6b34a39a1916f02b015afd2bb98587a3d Mon Sep 17 00:00:00 2001 From: Tim Sanders Date: Thu, 27 May 2021 16:55:30 +0000 Subject: [PATCH 01/22] Adding Manta module, associated pipeline & config changes --- pipeline/call-gSV.nf | 6 +++- pipeline/config/execute.config | 8 +++-- pipeline/config/lowmem.config | 6 +++- pipeline/config/methods.config | 1 + pipeline/config/midmem.config | 8 +++-- pipeline/modules/manta.nf | 54 ++++++++++++++++++++++++++++++++++ pipeline/modules/sha512.nf | 5 ++++ 7 files changed, 82 insertions(+), 6 deletions(-) create mode 100644 pipeline/modules/manta.nf diff --git a/pipeline/call-gSV.nf b/pipeline/call-gSV.nf index cac9512f..26501cad 100644 --- a/pipeline/call-gSV.nf +++ b/pipeline/call-gSV.nf @@ -34,6 +34,7 @@ Current Configuration: - tools: delly: ${params.delly_version} + manta: ${params.manta_version} bcftools: ${params.bcftools_version} vcftools: ${params.vcftools_version} rtgtools: ${params.rtgtools_version} @@ -48,6 +49,7 @@ Starting workflow... include { run_validate } from './modules/validation' include { call_gSV_Delly; call_gCNV_Delly } from './modules/delly' +include { call_gSV_Manta } from './modules/manta' include { convert_BCF2VCF_BCFtools as convert_gSV_BCF2VCF_BCFtools; convert_BCF2VCF_BCFtools as convert_gCNV_BCF2VCF_BCFtools } from './modules/bcftools' include { run_vcfstats_RTGTools } from './modules/rtgtools' include { run_vcf_validator_VCFtools } from './modules/vcftools' @@ -94,6 +96,7 @@ validation_channel = Channel workflow { run_validate(validation_channel) + call_gSV_Manta(input_bam_ch, params.reference_fasta, reference_fasta_index) call_gSV_Delly(input_bam_ch, params.reference_fasta, reference_fasta_index, params.exclusion_file) call_gCNV_Delly(input_bam_ch, call_gSV_Delly.out.bcf_sv_file, params.reference_fasta, reference_fasta_index, params.mappability_map) convert_gSV_BCF2VCF_BCFtools(call_gSV_Delly.out.bcf_sv_file, call_gSV_Delly.out.bam_sample_name, 'SV') @@ -102,5 +105,6 @@ workflow { run_vcfstats_RTGTools(convert_gSV_BCF2VCF_BCFtools.out.vcf_file, call_gSV_Delly.out.bam_sample_name) run_vcf_validator_VCFtools(convert_gSV_BCF2VCF_BCFtools.out.vcf_file, call_gSV_Delly.out.bam_sample_name) } - run_sha512sum(call_gSV_Delly.out.bcf_sv_file.mix(convert_gSV_BCF2VCF_BCFtools.out.vcf_file,call_gCNV_Delly.out.bcf_cnv_file,convert_gCNV_BCF2VCF_BCFtools.out.vcf_file)) + run_sha512sum(call_gSV_Delly.out.bcf_sv_file.mix(convert_gSV_BCF2VCF_BCFtools.out.vcf_file, call_gCNV_Delly.out.bcf_cnv_file, convert_gCNV_BCF2VCF_BCFtools.out.vcf_file, + call_gSV_Manta.out.vcf_small_indel_sv_file, call_gSV_Manta.out.vcf_diploid_sv_file, call_gSV_Manta.out.vcf_candidate_sv_file)) } diff --git a/pipeline/config/execute.config b/pipeline/config/execute.config index bb25b497..a390da5b 100644 --- a/pipeline/config/execute.config +++ b/pipeline/config/execute.config @@ -4,7 +4,11 @@ process { memory = 1.GB } withName: call_gSV_Delly { - cpus = 63 - memory = 940.GB + cpus = 31 + memory = 470.GB + } + withName: call_gSV_Manta { + cpus = 31 + memory = 470.GB } } \ No newline at end of file diff --git a/pipeline/config/lowmem.config b/pipeline/config/lowmem.config index 6bf4c59e..acdb0611 100644 --- a/pipeline/config/lowmem.config +++ b/pipeline/config/lowmem.config @@ -5,6 +5,10 @@ process { } withName: call_gSV_Delly { cpus = 1 - memory = 3.GB + memory = 2.GB + } + withName: call_gSV_Manta { + cpus = 1 + memory = 2.GB } } \ No newline at end of file diff --git a/pipeline/config/methods.config b/pipeline/config/methods.config index 047b5844..283a632f 100644 --- a/pipeline/config/methods.config +++ b/pipeline/config/methods.config @@ -95,6 +95,7 @@ methods.setup() params { // Pipeline tool versions delly_version = '0.8.7' + manta_version = '1.6.0' bcftools_version = '1.12' vcftools_version = '0.1.16' rtgtools_version = '3.12' diff --git a/pipeline/config/midmem.config b/pipeline/config/midmem.config index 799de112..3ff7d991 100644 --- a/pipeline/config/midmem.config +++ b/pipeline/config/midmem.config @@ -4,7 +4,11 @@ process { memory = 1.GB } withName: call_gSV_Delly { - cpus = 71 - memory = 130.GB + cpus = 35 + memory = 65.GB + } + withName: call_gSV_Manta { + cpus = 35 + memory = 65.GB } } \ No newline at end of file diff --git a/pipeline/modules/manta.nf b/pipeline/modules/manta.nf new file mode 100644 index 00000000..5fde3c27 --- /dev/null +++ b/pipeline/modules/manta.nf @@ -0,0 +1,54 @@ +#!/usr/bin/env nextflow + +def docker_image_manta = "blcdsdockerregistry/manta:${params.manta_version}" + +log.info """\ +------------------------------------ + M A N T A +------------------------------------ +Docker Images: +- docker_image_manta: ${docker_image_manta} +""" + +process call_gSV_Manta { + container docker_image_manta + + publishDir params.output_dir, + pattern: "MantaWorkflow/results", + mode: "copy", + saveAs: { "manta-${params.manta_version}/${file(it).getName()}" } + + publishDir params.output_log_dir, + pattern: ".command.*", + mode: "copy", + saveAs: { "call_gSV_Manta/${bam_sample_name}.log${file(it).getName()}" } + + input: + tuple val(patient), val(bam_sample_name), path(input_bam), path(input_bam_bai) + path(reference_fasta) + path(reference_fasta_fai) + + + output: + path("MantaWorkflow/results/variants/candidateSmallIndels.vcf.gz"), emit: vcf_small_indel_sv_file + path("MantaWorkflow/results/variants/candidateSmallIndels.vcf.gz.tbi") + path("MantaWorkflow/results/variants/diploidSV.vcf.gz"), emit: vcf_diploid_sv_file + path("MantaWorkflow/results/variants/diploidSV.vcf.gz.tbi") + path("MantaWorkflow/results/variants/candidateSV.vcf.gz"), emit: vcf_candidate_sv_file + path("MantaWorkflow/results/variants/candidateSV.vcf.gz.tbi") + //path "MANTA-${params.manta_version}_SV_${params.dataset_id}_${bam_sample_name}.vcf.gz", emit: vcf_sv_file + //path "MANTA-${params.manta_version}_SV_${params.dataset_id}_${bam_sample_name}.vcf.gz.tbi" + path "MantaWorkflow/results" + path ".command.*" + val bam_sample_name, emit: bam_sample_name + + """ + set -euo pipefail + configManta.py \ + --normalBam $input_bam \ + --referenceFasta $reference_fasta \ + --runDir MantaWorkflow + + MantaWorkflow/runWorkflow.py + """ +} \ No newline at end of file diff --git a/pipeline/modules/sha512.nf b/pipeline/modules/sha512.nf index b6b95147..8ca41d8c 100644 --- a/pipeline/modules/sha512.nf +++ b/pipeline/modules/sha512.nf @@ -23,6 +23,11 @@ process run_sha512sum { mode: "copy", saveAs: { "delly-${params.delly_version}/${file(it).getName()}" } + publishDir params.output_dir, + pattern: "*.vcf.gz*.sha512", + mode: "copy", + saveAs: { "manta-${params.manta_version}/results/variants/${file(it).getName()}" } + publishDir params.output_log_dir, pattern: ".command.*", mode: "copy", From 6a46abfaaffb6ccb19aabee0567006f1cf9c7fa1 Mon Sep 17 00:00:00 2001 From: Tim Sanders Date: Thu, 3 Jun 2021 20:46:29 +0000 Subject: [PATCH 02/22] Capitalized output directory to BCFtools --- pipeline/modules/bcftools.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pipeline/modules/bcftools.nf b/pipeline/modules/bcftools.nf index c659b624..98dc903b 100644 --- a/pipeline/modules/bcftools.nf +++ b/pipeline/modules/bcftools.nf @@ -16,7 +16,7 @@ process convert_BCF2VCF_BCFtools { publishDir params.output_dir, pattern: "*.vcf", mode: "copy", - saveAs: { "bcftools-${params.bcftools_version}/${file(it).getName()}" } + saveAs: { "BCFtools-${params.bcftools_version}/${file(it).getName()}" } publishDir params.output_log_dir, pattern: ".command.*", From c776e869d6b3485e9ccc579f3c551e42c68986a0 Mon Sep 17 00:00:00 2001 From: Tim Sanders Date: Thu, 3 Jun 2021 20:47:24 +0000 Subject: [PATCH 03/22] Capitalized output directory to VCFtools --- pipeline/modules/vcftools.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pipeline/modules/vcftools.nf b/pipeline/modules/vcftools.nf index 5edeb4a7..47962da3 100644 --- a/pipeline/modules/vcftools.nf +++ b/pipeline/modules/vcftools.nf @@ -16,7 +16,7 @@ process run_vcf_validator_VCFtools { publishDir params.output_dir, pattern: "*_validation.txt", mode: "copy", - saveAs: { "vcftools-${params.vcftools_version}/${file(it).getName()}" } + saveAs: { "VCFtools-${params.vcftools_version}/${file(it).getName()}" } publishDir params.output_log_dir, pattern: ".command.*", From 9f45fa8fec494bbfb5a08d2f6acefe417f19d87d Mon Sep 17 00:00:00 2001 From: Tim Sanders Date: Thu, 3 Jun 2021 20:48:26 +0000 Subject: [PATCH 04/22] Capitalized output directory --- pipeline/modules/manta.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pipeline/modules/manta.nf b/pipeline/modules/manta.nf index 5fde3c27..3ac8f333 100644 --- a/pipeline/modules/manta.nf +++ b/pipeline/modules/manta.nf @@ -16,7 +16,7 @@ process call_gSV_Manta { publishDir params.output_dir, pattern: "MantaWorkflow/results", mode: "copy", - saveAs: { "manta-${params.manta_version}/${file(it).getName()}" } + saveAs: { "Manta-${params.manta_version}/${file(it).getName()}" } publishDir params.output_log_dir, pattern: ".command.*", From 70e32d360f3a4dd4dbd9ad5e8a4ce6956cfa7c3e Mon Sep 17 00:00:00 2001 From: Tim Sanders Date: Thu, 3 Jun 2021 20:49:02 +0000 Subject: [PATCH 05/22] Capitalized output directory --- pipeline/modules/delly.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pipeline/modules/delly.nf b/pipeline/modules/delly.nf index 81242294..79c37258 100644 --- a/pipeline/modules/delly.nf +++ b/pipeline/modules/delly.nf @@ -17,7 +17,7 @@ process call_gSV_Delly { enabled: params.save_intermediate_files, pattern: "*.bcf*", mode: "copy", - saveAs: { "delly-${params.delly_version}/${file(it).getName()}" } + saveAs: { "Delly-${params.delly_version}/${file(it).getName()}" } publishDir params.output_log_dir, pattern: ".command.*", From c6ebfe2862f1cda9c6c68fab3c9ef3b807ffa0fb Mon Sep 17 00:00:00 2001 From: Tim Sanders Date: Thu, 3 Jun 2021 20:57:40 +0000 Subject: [PATCH 06/22] Capitalized output directory names --- pipeline/modules/sha512.nf | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/pipeline/modules/sha512.nf b/pipeline/modules/sha512.nf index 8ca41d8c..f48c66eb 100644 --- a/pipeline/modules/sha512.nf +++ b/pipeline/modules/sha512.nf @@ -16,17 +16,17 @@ process run_sha512sum { publishDir params.output_dir, pattern: "*.vcf.sha512", mode: "copy", - saveAs: { "bcftools-${params.bcftools_version}/${file(it).getName()}" } + saveAs: { "BCFtools-${params.bcftools_version}/${file(it).getName()}" } publishDir params.output_dir, pattern: "*.bcf.sha512", mode: "copy", - saveAs: { "delly-${params.delly_version}/${file(it).getName()}" } + saveAs: { "Delly-${params.delly_version}/${file(it).getName()}" } publishDir params.output_dir, pattern: "*.vcf.gz*.sha512", mode: "copy", - saveAs: { "manta-${params.manta_version}/results/variants/${file(it).getName()}" } + saveAs: { "Manta-${params.manta_version}/results/variants/${file(it).getName()}" } publishDir params.output_log_dir, pattern: ".command.*", From e70ebd9667e55676692b103b47f7abd73028ff26 Mon Sep 17 00:00:00 2001 From: Tim Sanders Date: Thu, 3 Jun 2021 23:47:37 +0000 Subject: [PATCH 07/22] Added run_delly and run_manta to config --- pipeline/config/nextflow.config | 2 ++ 1 file changed, 2 insertions(+) diff --git a/pipeline/config/nextflow.config b/pipeline/config/nextflow.config index a7440f48..09d1a052 100644 --- a/pipeline/config/nextflow.config +++ b/pipeline/config/nextflow.config @@ -23,6 +23,8 @@ params { exclusion_file = '/path/to/exclusion.tsv' mappability_map = '/path/to/mappability_map' map_qual = 20 // min. paired-end (PE) mapping quality for Delly + run_delly = true + run_manta = true run_qc = true save_intermediate_files = true output_dir = '/path/to/outputs' From 5cee95faf1e6924a68dd83458691a29b1a7d8a75 Mon Sep 17 00:00:00 2001 From: Tim Sanders Date: Mon, 7 Jun 2021 19:19:26 +0000 Subject: [PATCH 08/22] Capitalized Delly tool name in output --- pipeline/modules/delly.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pipeline/modules/delly.nf b/pipeline/modules/delly.nf index 79c37258..8a4627bb 100644 --- a/pipeline/modules/delly.nf +++ b/pipeline/modules/delly.nf @@ -56,7 +56,7 @@ process call_gCNV_Delly { enabled: params.save_intermediate_files, pattern: "*.bcf*", mode: "copy", - saveAs: { "delly-${params.delly_version}/${file(it).getName()}" } + saveAs: { "Delly-${params.delly_version}/${file(it).getName()}" } publishDir params.output_log_dir, pattern: ".command.*", From f71bfd4dcd5411f2ae77671896ff6d1c0999bf08 Mon Sep 17 00:00:00 2001 From: Tim Sanders Date: Mon, 7 Jun 2021 19:20:23 +0000 Subject: [PATCH 09/22] Added Manta process to pipeline; added SV tool params --- pipeline/call-gSV.nf | 43 +++++++++++++++++++++++++++---------------- 1 file changed, 27 insertions(+), 16 deletions(-) diff --git a/pipeline/call-gSV.nf b/pipeline/call-gSV.nf index 26501cad..a6a3200e 100644 --- a/pipeline/call-gSV.nf +++ b/pipeline/call-gSV.nf @@ -31,6 +31,8 @@ Current Configuration: save_intermediate_files: ${params.save_intermediate_files} run_qc: ${params.run_qc} map_qual: ${params.map_qual} + run_delly: ${params.run_delly} + run_manta: ${params.run_manta} - tools: delly: ${params.delly_version} @@ -53,7 +55,7 @@ include { call_gSV_Manta } from './modules/manta' include { convert_BCF2VCF_BCFtools as convert_gSV_BCF2VCF_BCFtools; convert_BCF2VCF_BCFtools as convert_gCNV_BCF2VCF_BCFtools } from './modules/bcftools' include { run_vcfstats_RTGTools } from './modules/rtgtools' include { run_vcf_validator_VCFtools } from './modules/vcftools' -include { run_sha512sum } from './modules/sha512' +include { run_sha512sum as run_sha512sum_Delly; run_sha512sum as run_sha512sum_Manta } from './modules/sha512' input_bam_ch = Channel .fromPath(params.input_csv, checkIfExists:true) @@ -69,19 +71,24 @@ input_bam_ch = Channel if (!params.reference_fasta) { // error out - must provide a reference FASTA file error "***Error: You must specify a reference FASTA file***" -} + } if (!params.exclusion_file) { // error out - must provide exclusion file error "***Error: You must provide an exclusion file***" -} + } + +if (!params.run_delly && !params.run_manta) { + // error out - must specify a valid SV caller + error "***Error: You must specify either Delly or Manta***" + } if (params.reference_fasta_index) { reference_fasta_index = params.reference_fasta_index -} + } else { reference_fasta_index = "${params.reference_fasta}.fai" -} + } // Create channel for validation validation_channel = Channel @@ -96,15 +103,19 @@ validation_channel = Channel workflow { run_validate(validation_channel) - call_gSV_Manta(input_bam_ch, params.reference_fasta, reference_fasta_index) - call_gSV_Delly(input_bam_ch, params.reference_fasta, reference_fasta_index, params.exclusion_file) - call_gCNV_Delly(input_bam_ch, call_gSV_Delly.out.bcf_sv_file, params.reference_fasta, reference_fasta_index, params.mappability_map) - convert_gSV_BCF2VCF_BCFtools(call_gSV_Delly.out.bcf_sv_file, call_gSV_Delly.out.bam_sample_name, 'SV') - convert_gCNV_BCF2VCF_BCFtools(call_gCNV_Delly.out.bcf_cnv_file, call_gCNV_Delly.out.bam_sample_name, 'CNV') - if (params.run_qc) { - run_vcfstats_RTGTools(convert_gSV_BCF2VCF_BCFtools.out.vcf_file, call_gSV_Delly.out.bam_sample_name) - run_vcf_validator_VCFtools(convert_gSV_BCF2VCF_BCFtools.out.vcf_file, call_gSV_Delly.out.bam_sample_name) - } - run_sha512sum(call_gSV_Delly.out.bcf_sv_file.mix(convert_gSV_BCF2VCF_BCFtools.out.vcf_file, call_gCNV_Delly.out.bcf_cnv_file, convert_gCNV_BCF2VCF_BCFtools.out.vcf_file, - call_gSV_Manta.out.vcf_small_indel_sv_file, call_gSV_Manta.out.vcf_diploid_sv_file, call_gSV_Manta.out.vcf_candidate_sv_file)) + if (params.run_manta) { + call_gSV_Manta(input_bam_ch, params.reference_fasta, reference_fasta_index) + run_sha512sum_Manta(call_gSV_Manta.out.vcf_small_indel_sv_file.mix(call_gSV_Manta.out.vcf_diploid_sv_file, call_gSV_Manta.out.vcf_candidate_sv_file)) + } + if (params.run_delly) { + call_gSV_Delly(input_bam_ch, params.reference_fasta, reference_fasta_index, params.exclusion_file) + call_gCNV_Delly(input_bam_ch, call_gSV_Delly.out.bcf_sv_file, params.reference_fasta, reference_fasta_index, params.mappability_map) + convert_gSV_BCF2VCF_BCFtools(call_gSV_Delly.out.bcf_sv_file, call_gSV_Delly.out.bam_sample_name, 'SV') + convert_gCNV_BCF2VCF_BCFtools(call_gCNV_Delly.out.bcf_cnv_file, call_gCNV_Delly.out.bam_sample_name, 'CNV') + if (params.run_qc) { + run_vcfstats_RTGTools(convert_gSV_BCF2VCF_BCFtools.out.vcf_file, call_gSV_Delly.out.bam_sample_name) + run_vcf_validator_VCFtools(convert_gSV_BCF2VCF_BCFtools.out.vcf_file, call_gSV_Delly.out.bam_sample_name) + } + run_sha512sum_Delly(call_gSV_Delly.out.bcf_sv_file.mix(convert_gSV_BCF2VCF_BCFtools.out.vcf_file, call_gCNV_Delly.out.bcf_cnv_file, convert_gCNV_BCF2VCF_BCFtools.out.vcf_file)) + } } From 775c3be588cd22d110803e2f661e33893f8bdebb Mon Sep 17 00:00:00 2001 From: Tim Sanders <43756632+timothyjsanders@users.noreply.github.com> Date: Mon, 7 Jun 2021 12:51:25 -0700 Subject: [PATCH 10/22] Added Manta to tools and description --- metadata.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/metadata.yaml b/metadata.yaml index 270e48f4..b24e84ab 100644 --- a/metadata.yaml +++ b/metadata.yaml @@ -1,11 +1,11 @@ --- Category: "pipeline" -Description: "a pipeline for calling structural variants and copy number variants utilizing Delly" +Description: "a pipeline for calling structural variants and copy number variants utilizing Delly and Manta" Maintainers: "Boutros Lab Infrastructure BoutrosLabInfrastructure@mednet.ucla.edu" Contributors: ["Yael Berkovich", "Tim Sanders"] Languages: ["Nextflow", "Docker"] Dependencies: ["Java", "Nextflow", "Docker"] References: "https://confluence.mednet.ucla.edu/display/BOUTROSLAB/Guide+to+Nextflow" -Tools: ["Delly:v0.8.7", "BCFtools:v1.12", "VCFtools:v0.1.16", "RTG-tools:v3.12", "Validate-nf:v2.1.0"] +Tools: ["Delly:v0.8.7", "Manta:v1.6.0", "BCFtools:v1.12", "VCFtools:v0.1.16", "RTG-tools:v3.12", "Validate-nf:v2.1.0"] Engineering_Owner: [] Scientific_Owner: [] From c08be208308e4e1f05150a68b1c06156a5d30542 Mon Sep 17 00:00:00 2001 From: Tim Sanders <43756632+timothyjsanders@users.noreply.github.com> Date: Mon, 7 Jun 2021 12:55:00 -0700 Subject: [PATCH 11/22] Added version 3.0.0 changelog information --- CHANGELOG.md | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index ed5ccd3e..5feb7b84 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,6 +1,15 @@ # Changelog All notable changes to the call-gSV pipeline. +## [3.0.0] - 2021-06-08 +### Added +- Added ability to call germline SVs with Manta +- Added parameters to control which SV caller is used (run_delly & run_manta) +- Added pipeline version from manifest to pipeline logging output + +### Changed +- Changed output directories to correspond with tool name casing + ## [2.2.0] - 2021-05-07 ### Changed - Updated modules to point to tool specific Docker Hub repos From 545484dcd2b9e2100c29674a87493df5c781f892 Mon Sep 17 00:00:00 2001 From: Tim Sanders <43756632+timothyjsanders@users.noreply.github.com> Date: Mon, 7 Jun 2021 12:57:38 -0700 Subject: [PATCH 12/22] Added run_delly and run_manta to nextflow.config --- pipeline/config/nextflow.config | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/pipeline/config/nextflow.config b/pipeline/config/nextflow.config index a7440f48..864627f6 100644 --- a/pipeline/config/nextflow.config +++ b/pipeline/config/nextflow.config @@ -5,8 +5,8 @@ manifest { nextflowVersion = '>=20.07.1' author = 'Tim Sanders & Yael Berkovich' homePage = 'https://github.com/uclahs-cds/pipeline-call-gSV' - description = 'A pipeline to call structural variants utilizing Delly' - version = '2.2.0' + description = 'A pipeline to call structural variants utilizing Delly and Manta' + version = '3.0.0' } params { @@ -23,6 +23,9 @@ params { exclusion_file = '/path/to/exclusion.tsv' mappability_map = '/path/to/mappability_map' map_qual = 20 // min. paired-end (PE) mapping quality for Delly + // run_delly or run_manta (or both) must be set to true + run_delly = true + run_manta = true run_qc = true save_intermediate_files = true output_dir = '/path/to/outputs' From ad3ec61d5772c26fd5c8bd897f083b9ea4c52d80 Mon Sep 17 00:00:00 2001 From: Tim Sanders Date: Mon, 7 Jun 2021 13:17:34 -0700 Subject: [PATCH 13/22] Updated flowchart diagram with Manta flow --- call-gSV-flowchart-diagram.drawio.svg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/call-gSV-flowchart-diagram.drawio.svg b/call-gSV-flowchart-diagram.drawio.svg index 2e1ae1bc..6e3f3551 100644 --- a/call-gSV-flowchart-diagram.drawio.svg +++ b/call-gSV-flowchart-diagram.drawio.svg @@ -1,3 +1,3 @@ -
Sorted
BAM and
BAM Index
Sorted...
Validate Inputs
Validate Inputs
Call Structural Variants
Call Structural...
Check Quality
Check Quality
Validate Outputs
Validate Outputs
BCF and VCF
BCF and VCF
Create Sha512
Create Sha512
Call Copy Number Variants
Call Copy Numbe...Viewer does not support full SVG 1.1 \ No newline at end of file +
Sorted
BAM and
BAM Index
Sorted...
Validate Inputs
Validate Inputs
Call Structural Variants (Delly)
Call Structural...
Check Quality
Check Quality
Validate Outputs
Validate Outputs
BCF and VCF
BCF and VCF
Create SHA-512
Create SHA-512
Call Copy Number Variants
Call Copy Numbe...
Call Structural Variants (Manta)
Call Structural...Viewer does not support full SVG 1.1 \ No newline at end of file From f83beb248289f0a6bfe02c104b584bcd7b5784e3 Mon Sep 17 00:00:00 2001 From: Tim Sanders <43756632+timothyjsanders@users.noreply.github.com> Date: Mon, 7 Jun 2021 14:28:36 -0700 Subject: [PATCH 14/22] Updating readme with Manta documentation --- README.md | 35 +++++++++++++++++++++-------------- 1 file changed, 21 insertions(+), 14 deletions(-) diff --git a/README.md b/README.md index d4789f4a..f45b4c1f 100644 --- a/README.md +++ b/README.md @@ -20,7 +20,7 @@ ## Overview -The call-gSV nextflow pipeline, calls structural variants and copy number variants utilizing [Delly](https://github.com/dellytools/delly). It is suitable for detecting copy-number variable deletion and tandem duplication events as well as balanced rearrangements such as inversions or reciprocal translocations and validates the output quality with [BCFtools](https://github.com/samtools/bcftools). The pipeline has been engineered to run in a 4 layer stack in a cloud-based scalable environment of CycleCloud, Slurm, Nextflow and Docker. Additionally it has been validated with the SMC-HET dataset and reference GRCh38 reference genome, where paired-end FASTQ's were created with BAM Surgeon. +The call-gSV nextflow pipeline, calls structural variants and copy number variants utilizing [Delly](https://github.com/dellytools/delly) and [Manta](https://github.com/Illumina/manta). It is suitable for detecting copy-number variable deletion and tandem duplication events as well as balanced rearrangements such as inversions or reciprocal translocations and validates the output quality with [BCFtools](https://github.com/samtools/bcftools). The pipeline has been engineered to run in a 4 layer stack in a cloud-based scalable environment of CycleCloud, Slurm, Nextflow and Docker. Additionally it has been validated with the SMC-HET dataset and reference GRCh38 reference genome, where paired-end FASTQ's were created with BAM Surgeon. Developer's Notes: @@ -28,11 +28,11 @@ The call-gSV nextflow pipeline, calls structural variants and copy number varian ### Node Specific Config File Settings -| Config File | Available Node cpus / memory | Designated Process 1; cpus / memory | Designated Process 2; cpus / memory | -|:------------|:---------|:-------------------------|:-------------------------| -| `lowmem.config` | 2 / 3 GB | delly_call_sv; 1 / 3 GB | validate_file; 1 / 1 GB | -| `midmem.config` | 72 / 136.8 GB | delly_call_sv; 71 / 130 GB | validate_file; 1 / 1 GB | -| `execute.config` | 64 / 950 GB | delly_call_sv; 63 / 940 GB | validate_file; 1 / 1 GB | +| Config File | Available Node cpus / memory | Designated Process 1; cpus / memory | Designated Process 3; cpus / memory | Designated Process 2; cpus / memory | +|:------------|:---------|:-------------------------|:-------------------------|:-------------------------| +| `lowmem.config` | 2 / 3 GB | call_gSV_Delly; 1 / 2 GB | call_gSV_Manta; 1 / 2 GB | validate_file; 1 / 1 GB | +| `midmem.config` | 72 / 136.8 GB | call_gSV_Delly; 35 / 65 GB | call_gSV_Manta; 35 / 65 GB | validate_file; 1 / 1 GB | +| `execute.config` | 64 / 950 GB | call_gSV_Delly; 31 / 470 GB | call_gSV_Manta; 31 / 470 GB | validate_file; 1 / 1 GB | --- ## How To Run @@ -61,14 +61,18 @@ A directed acyclic graph of your pipeline. ### 1. Calling Structural Variants -The first step of the pipeline requires an aligned and sorted BAM file and BAM index as an input for variant calling with [Delly.](https://github.com/dellytools/delly) Delly combines short-range and long-range paired-end mapping and split-read analysis for the discovery of balanced and unbalanced structural variants at single-nucleotide breakpoint resolution (deletions, tandem duplications, inversions and translocations.) Structural variants are called, annotated and merged into a single BCF file. A default exclude map of Delly can be incorporated as an input which removes the telomeric and centromeric regions of all human chromosomes since these regions cannot be accurately analyzed with short-read data. +The first step of the pipeline requires an aligned and sorted BAM file and BAM index as an input for variant calling with [Delly](https://github.com/dellytools/delly) or [Manta](https://github.com/Illumina/manta). Delly combines short-range and long-range paired-end mapping and split-read analysis for the discovery of balanced and unbalanced structural variants at single-nucleotide breakpoint resolution (deletions, tandem duplications, inversions and translocations.) Structural variants are called, annotated and merged into a single BCF file. A default exclude map of Delly can be incorporated as an input which removes the telomeric and centromeric regions of all human chromosomes since these regions cannot be accurately analyzed with short-read data. +Manta calls structural variants (SVs) and indels from mapped paired-end sequencing reads. It is optimized for analysis of germline variation in small sets of individuals and somatic variation in tumor/normal sample pairs. Manta discovers, assembles and scores large-scale SVs, medium-sized indels and large insertions within a single efficient workflow. Currently the following filters are applied and or considered for application and parameterization in subsequent releases: +
+**Delly** * **map-qual:** >= 20 (Applied / Parameterized) * **pe:** >= 5 (Not yet Applied / Non-parameterized) * **sr:** >= 5 (Not yet Applied / Non-parameterized) * **keep_imprecise:** >= true (Not yet Applied / Non-parameterized) + ### 2. Calling Copy Number Variants The second step of the pipeline identifies any found copy number variants (CNVs). To do this, Delly requires an aligned and sorted BAM file and BAM index as an input, as well as the BCF output from the initial structural variant calling (to refine breakpoints) and a mappability map. Any CNVs identified are annotated and output as a single BCF file. @@ -89,7 +93,7 @@ Currently the following filters are applied and or considered for application an ### 3. Check Output Quality -VCF files are generated from the BCFs to run the vcf-validate command from [VCFTools](https://vcftools.github.io/perl_module.html#vcf-validator) and vcfstats from [RTGTools](https://cdn.rawgit.com/RealTimeGenomics/rtg-tools/master/installer/resources/tools/RTGOperationsManual/rtg_command_reference.html#vcfstats). Outputs from both provide preliminary summary statistics that can be viewed and evaluated in preparation for downstream cohort-wide re-calling and re-genotyping. +For Delly, VCF files are generated from the BCFs to run the vcf-validate command from [VCFTools](https://vcftools.github.io/perl_module.html#vcf-validator) and vcfstats from [RTGTools](https://cdn.rawgit.com/RealTimeGenomics/rtg-tools/master/installer/resources/tools/RTGOperationsManual/rtg_command_reference.html#vcfstats). Outputs from both provide preliminary summary statistics that can be viewed and evaluated in preparation for downstream cohort-wide re-calling and re-genotyping. In the Manta branch of the pipeline, a stats directory is generated under the specific output directory /Manta-/results/stats where information can be found regarding the SVs identified. --- @@ -119,7 +123,9 @@ VCF files are generated from the BCFs to run the vcf-validate command from [VCFT | `exclusion_file` | yes | path | Absolute path to the delly reference genome `exclusion` file utilized to remove suggested regions for structural variant calling. On Slurm/SGE, an HG38 exclusion file is located at /[hot\|data]/ref/hg38/delly/human.hg38.excl.tsv | | `mappability_map` | yes | path | Absolute path to the delly mappability map to support GC and mappability fragment correction in CNV calling | | `map_qual` | no | path | minimum paired-end (PE) mapping quaility threshold for Delly). | -| `run_qc` | no | boolean | Optional parameter to indicate whether subsequent quality checks should be run. Default value is false. | +| `run_delly` | true | boolean | Whether or not the workflow should run Delly (either run_delly or run_manta must be set to true) | +| `run_manta` | true | boolean | Whether or not the workflow should run Manta (either run_delly or run_manta must be set to true) | +| `run_qc` | no | boolean | Optional parameter to indicate whether subsequent quality checks should be run on Delly outputs. Default value is false. | | `save_intermediate_files` | yes | boolean | Optional parameter to indicate whether intermediate files will be saved. Default value is true. | | `output_dir` | yes | path | Absolute path to the directory where the output files to be saved. | `temp_dir` | yes | path | Absolute path to the directory where the nextflow's intermediate files are saved. | @@ -131,7 +137,7 @@ VCF files are generated from the BCFs to run the vcf-validate command from [VCFT | Output | Output Type | Description | |:-------|:---------|:------------| | `.bcf` | final | Binary VCF output format with structural variants if found. | -| `.vcf` | intermediate | VCF output format with structural variants if found.| +| `.vcf` | intermediate | VCF output format with structural variants if found. If output by Manta, these VCFs will be compressed. | | `.bcf.csi` | final | CSI-format index for BAM files. | | `.validate.txt` | final | output file from vcf-validator. | | `.stats.txt` | final | output file from RTG Tools. | @@ -205,7 +211,8 @@ Included is a template for validating your input files. For more information on ## References 1. [Rausch T, Zichner T, Schlattl A, Stütz AM, Benes V, Korbel JO. DELLY: structural variant discovery by integrated paired-end and split-read analysis. Bioinformatics. 2012;28(18):i333-i339. doi:10.1093/bioinformatics/bts378](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3436805/) -2. [VCFtools - vcf-validator](https://vcftools.github.io/perl_module.html#vcf-validator) -3. [Real Time Genomics RTG Tools Operations Manual - vcfstats](https://cdn.rawgit.com/RealTimeGenomics/rtg-tools/master/installer/resources/tools/RTGOperationsManual/rtg_command_reference.html#vcfstats) -4. [Boutros Lab -CallSV Quality Control pipeline]() -5. [The 1000 Genomes Project Consortium., Corresponding authors., Auton, A. et al. A global reference for human genetic variation. Nature 526, 68–74 (2015). https://doi.org/10.1038/nature15393](https://www.nature.com/articles/nature15393) +2. Chen, X. et al. (2016) Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications. Bioinformatics, 32, 1220-1222. [doi:10.1093/bioinformatics/btv710](https://academic.oup.com/bioinformatics/article/32/8/1220/1743909) +3. [VCFtools - vcf-validator](https://vcftools.github.io/perl_module.html#vcf-validator) +4. [Real Time Genomics RTG Tools Operations Manual - vcfstats](https://cdn.rawgit.com/RealTimeGenomics/rtg-tools/master/installer/resources/tools/RTGOperationsManual/rtg_command_reference.html#vcfstats) +5. [Boutros Lab -CallSV Quality Control pipeline]() +6. [The 1000 Genomes Project Consortium., Corresponding authors., Auton, A. et al. A global reference for human genetic variation. Nature 526, 68–74 (2015). https://doi.org/10.1038/nature15393](https://www.nature.com/articles/nature15393) From a21332df3b7dfd2badff2a51212e4f425d9661b9 Mon Sep 17 00:00:00 2001 From: Tim Sanders <43756632+timothyjsanders@users.noreply.github.com> Date: Mon, 7 Jun 2021 14:39:19 -0700 Subject: [PATCH 15/22] Updated table headers --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index f45b4c1f..8353baa2 100644 --- a/README.md +++ b/README.md @@ -28,7 +28,7 @@ The call-gSV nextflow pipeline, calls structural variants and copy number varian ### Node Specific Config File Settings -| Config File | Available Node cpus / memory | Designated Process 1; cpus / memory | Designated Process 3; cpus / memory | Designated Process 2; cpus / memory | +| Config File | Available Node cpus / memory | Designated Process 1; cpus / memory | Designated Process 2; cpus / memory | Designated Process 3; cpus / memory | |:------------|:---------|:-------------------------|:-------------------------|:-------------------------| | `lowmem.config` | 2 / 3 GB | call_gSV_Delly; 1 / 2 GB | call_gSV_Manta; 1 / 2 GB | validate_file; 1 / 1 GB | | `midmem.config` | 72 / 136.8 GB | call_gSV_Delly; 35 / 65 GB | call_gSV_Manta; 35 / 65 GB | validate_file; 1 / 1 GB | From 3cbce95b17d492b79e036e845d3746198c717dfe Mon Sep 17 00:00:00 2001 From: Tim Sanders Date: Wed, 9 Jun 2021 23:50:50 +0000 Subject: [PATCH 16/22] Updated validation docker to 2.1.5 --- pipeline/config/methods.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pipeline/config/methods.config b/pipeline/config/methods.config index 283a632f..176af723 100644 --- a/pipeline/config/methods.config +++ b/pipeline/config/methods.config @@ -99,7 +99,7 @@ params { bcftools_version = '1.12' vcftools_version = '0.1.16' rtgtools_version = '3.12' - validate_version = '2.1.0' + validate_version = '2.1.5' sha512_version = '0.1' } From 51c9fc9c119e1c12483513a00c3f6319905f2b37 Mon Sep 17 00:00:00 2001 From: Tim Sanders Date: Wed, 9 Jun 2021 23:51:59 +0000 Subject: [PATCH 17/22] Updated validation version to match methods.config (2.1.5) --- metadata.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/metadata.yaml b/metadata.yaml index b24e84ab..43074d11 100644 --- a/metadata.yaml +++ b/metadata.yaml @@ -6,6 +6,6 @@ Contributors: ["Yael Berkovich", "Tim Sanders"] Languages: ["Nextflow", "Docker"] Dependencies: ["Java", "Nextflow", "Docker"] References: "https://confluence.mednet.ucla.edu/display/BOUTROSLAB/Guide+to+Nextflow" -Tools: ["Delly:v0.8.7", "Manta:v1.6.0", "BCFtools:v1.12", "VCFtools:v0.1.16", "RTG-tools:v3.12", "Validate-nf:v2.1.0"] +Tools: ["Delly:v0.8.7", "Manta:v1.6.0", "BCFtools:v1.12", "VCFtools:v0.1.16", "RTG-tools:v3.12", "Validate-nf:v2.1.5"] Engineering_Owner: [] Scientific_Owner: [] From 702328d2439cabcf1d326d38d8cdac40bde17577 Mon Sep 17 00:00:00 2001 From: Tim Sanders Date: Thu, 10 Jun 2021 21:35:02 +0000 Subject: [PATCH 18/22] Added table with all Delly default parameters --- README.md | 19 ++++++++++++------- 1 file changed, 12 insertions(+), 7 deletions(-) diff --git a/README.md b/README.md index 8353baa2..1ff32989 100644 --- a/README.md +++ b/README.md @@ -64,14 +64,19 @@ A directed acyclic graph of your pipeline. The first step of the pipeline requires an aligned and sorted BAM file and BAM index as an input for variant calling with [Delly](https://github.com/dellytools/delly) or [Manta](https://github.com/Illumina/manta). Delly combines short-range and long-range paired-end mapping and split-read analysis for the discovery of balanced and unbalanced structural variants at single-nucleotide breakpoint resolution (deletions, tandem duplications, inversions and translocations.) Structural variants are called, annotated and merged into a single BCF file. A default exclude map of Delly can be incorporated as an input which removes the telomeric and centromeric regions of all human chromosomes since these regions cannot be accurately analyzed with short-read data. Manta calls structural variants (SVs) and indels from mapped paired-end sequencing reads. It is optimized for analysis of germline variation in small sets of individuals and somatic variation in tumor/normal sample pairs. Manta discovers, assembles and scores large-scale SVs, medium-sized indels and large insertions within a single efficient workflow. -Currently the following filters are applied and or considered for application and parameterization in subsequent releases: +Currently the following filters are applied by Delly. Parameters with a "call-gSV default" can be updated in the nextflow.config file. +
+| Parameter | Delly default | call-gSV default | Description | +|:------------|:----------|:-------------------------|-------------| +| `svtype` | ALL | | SV type to compute (DEL, INS, DUP, INV, BND, ALL) | +| `map-qual` | 20 | 20 | Minimum paired-end (PE) mapping quality | +| `qual-tra` | 20 | | Minimum PE quality for translocation | +| `mad-cutoff` | 9 | | Insert size cutoff, median+s*MAD (deletions only) | +| `minclip` | 25 | | Minimum clipping length | +| `min-clique-size` | 2 | | Minimum PE/SR clique size | +| `minrefsep` | 25 | | Minimum reference separation | +| `maxreadsep` | 40 | | Maximum read separation |
-**Delly** -* **map-qual:** >= 20 (Applied / Parameterized) -* **pe:** >= 5 (Not yet Applied / Non-parameterized) -* **sr:** >= 5 (Not yet Applied / Non-parameterized) -* **keep_imprecise:** >= true (Not yet Applied / Non-parameterized) - ### 2. Calling Copy Number Variants From 04216f73bf4e6e60811669541bba9f25962b1cae Mon Sep 17 00:00:00 2001 From: Tim Sanders Date: Thu, 10 Jun 2021 22:03:32 +0000 Subject: [PATCH 19/22] Modified copy number variant parameters into table format --- README.md | 32 ++++++++++++++++++-------------- 1 file changed, 18 insertions(+), 14 deletions(-) diff --git a/README.md b/README.md index 1ff32989..a084c092 100644 --- a/README.md +++ b/README.md @@ -64,7 +64,7 @@ A directed acyclic graph of your pipeline. The first step of the pipeline requires an aligned and sorted BAM file and BAM index as an input for variant calling with [Delly](https://github.com/dellytools/delly) or [Manta](https://github.com/Illumina/manta). Delly combines short-range and long-range paired-end mapping and split-read analysis for the discovery of balanced and unbalanced structural variants at single-nucleotide breakpoint resolution (deletions, tandem duplications, inversions and translocations.) Structural variants are called, annotated and merged into a single BCF file. A default exclude map of Delly can be incorporated as an input which removes the telomeric and centromeric regions of all human chromosomes since these regions cannot be accurately analyzed with short-read data. Manta calls structural variants (SVs) and indels from mapped paired-end sequencing reads. It is optimized for analysis of germline variation in small sets of individuals and somatic variation in tumor/normal sample pairs. Manta discovers, assembles and scores large-scale SVs, medium-sized indels and large insertions within a single efficient workflow. -Currently the following filters are applied by Delly. Parameters with a "call-gSV default" can be updated in the nextflow.config file. +Currently the following filters are applied by Delly when calling structural variants. Parameters with a "call-gSV default" can be updated in the nextflow.config file.
| Parameter | Delly default | call-gSV default | Description | |:------------|:----------|:-------------------------|-------------| @@ -82,19 +82,23 @@ Currently the following filters are applied by Delly. Parameters with a "call-gS The second step of the pipeline identifies any found copy number variants (CNVs). To do this, Delly requires an aligned and sorted BAM file and BAM index as an input, as well as the BCF output from the initial structural variant calling (to refine breakpoints) and a mappability map. Any CNVs identified are annotated and output as a single BCF file. -Currently the following filters are applied and or considered for application and parameterization in subsequent releases: -* **quality:** = 10 (Applied / Non-parameterized) -* **ploidy:** = 2 (Applied / Non-parameterized) -* **sdrd:** = 2 (Applied / Non-parameterized) -* **cn-offset** = 0.100000001 (Applied / Non-parameterized) -* **cnv-size** = 1000 (Applied / Non-parameterized) -* **window-size** = 10000 (Applied / Non-parameterized) -* **window-offset** = 10000 (Applied / Non-parameterized) -* **fraction-window** = 0.25 (Applied / Non-parameterized) -* **scan-window** = 10000 (Applied / Non-parameterized) -* **fraction-unique** = 0.800000012 (Applied / Non-parameterized) -* **mad-cutoff** = 3 (Applied / Non-parameterized) -* **percentile** = 0.000500000024 (Applied / Non-parameterized) +Currently the following filters are applied by Delly when calling copy number variants. Parameters with a "call-gSV default" can be updated in the nextflow.config file. +
+| Parameter | Delly default | call-gSV default | Description | +|:------------|:----------|:-------------------------|-------------| +| `quality` | 10 | | Minimum mapping quality | +| `ploidy` | 2 | | Baseline ploidy | +| `sdrd` | 2 | | Minimum SD read-depth shift | +| `cn-offset` | 0.100000001 | | Minimum CN offset | +| `cnv-size` | 1000 | | Minimum CNV size | +| `window-size` | 10000 | | Window size | +| `window-offset` | 10000 | | Window offset | +| `fraction-window` | 0.25 | | Minimum callable window fraction [0.1] | +| `scan-window` | 10000 | | Scanning window size | +| `fraction-unique` | 0.800000012 | | Uniqueness filter for scan windows [0,1] | +| `mad-cutoff` | 3 | | Median + 3 * mad count cutoff | +| `percentile` | 0.000500000024 | | Excl. extreme GC fraction | +
### 3. Check Output Quality From 652425e426eb36183274501208fb57dcfbba6eef Mon Sep 17 00:00:00 2001 From: Tim Sanders Date: Thu, 10 Jun 2021 22:08:47 +0000 Subject: [PATCH 20/22] Fixed default delly call map-qual value --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index a084c092..671101f3 100644 --- a/README.md +++ b/README.md @@ -69,7 +69,7 @@ Currently the following filters are applied by Delly when calling structural var | Parameter | Delly default | call-gSV default | Description | |:------------|:----------|:-------------------------|-------------| | `svtype` | ALL | | SV type to compute (DEL, INS, DUP, INV, BND, ALL) | -| `map-qual` | 20 | 20 | Minimum paired-end (PE) mapping quality | +| `map-qual` | 1 | 20 | Minimum paired-end (PE) mapping quality | | `qual-tra` | 20 | | Minimum PE quality for translocation | | `mad-cutoff` | 9 | | Insert size cutoff, median+s*MAD (deletions only) | | `minclip` | 25 | | Minimum clipping length | From aeebbd5b14c70aaaba4c3af7ac6e865161b2cedb Mon Sep 17 00:00:00 2001 From: Tim Sanders Date: Thu, 10 Jun 2021 22:23:36 +0000 Subject: [PATCH 21/22] Fixed typo in CNV params table --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 671101f3..5a781552 100644 --- a/README.md +++ b/README.md @@ -93,7 +93,7 @@ Currently the following filters are applied by Delly when calling copy number v | `cnv-size` | 1000 | | Minimum CNV size | | `window-size` | 10000 | | Window size | | `window-offset` | 10000 | | Window offset | -| `fraction-window` | 0.25 | | Minimum callable window fraction [0.1] | +| `fraction-window` | 0.25 | | Minimum callable window fraction [0,1] | | `scan-window` | 10000 | | Scanning window size | | `fraction-unique` | 0.800000012 | | Uniqueness filter for scan windows [0,1] | | `mad-cutoff` | 3 | | Median + 3 * mad count cutoff | From da9990218c8affc765591ae2c7eeecb4b0fb4dd6 Mon Sep 17 00:00:00 2001 From: Tim Sanders Date: Thu, 10 Jun 2021 22:25:36 +0000 Subject: [PATCH 22/22] Changed release 3.0.0 to unreleased --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 5feb7b84..3803a9eb 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,7 +1,7 @@ # Changelog All notable changes to the call-gSV pipeline. -## [3.0.0] - 2021-06-08 +## [Unreleased] ### Added - Added ability to call germline SVs with Manta - Added parameters to control which SV caller is used (run_delly & run_manta)