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kfdrc-jointgenotyping-refinement-workflow.cwl
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kfdrc-jointgenotyping-refinement-workflow.cwl
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cwlVersion: v1.2
class: Workflow
id: kfdrc-jointgenotyping-refinement-workflow
label: Kids First DRC Joint Genotyping Workflow
doc: |
# Kids First DRC Joint Genotyping Workflow
Kids First Data Resource Center Joint Genotyping Workflow (cram-to-deNovoGVCF). Cohort sample variant calling and genotype refinement.
Note: The DNA annotation has been significantly upgraded since v2.2.3, if you'd like to use the old version, revert to that release.
Using existing gVCFs, likely from GATK Haplotype Caller, we follow this workflow: [Germline short variant discovery (SNPs + Indels)](https://software.broadinstitute.org/gatk/best-practices/workflow?id=11145), to create family joint calling and joint trios (typically mother-father-child) variant calls. Peddy is run to raise any potential issues in family relation definitions and sex assignment.
If you would like to run this workflow using the cavatica public app, a basic primer on running public apps can be found [here](https://www.notion.so/d3b/Starting-From-Scratch-Running-Cavatica-af5ebb78c38a4f3190e32e67b4ce12bb).
Alternatively, if you'd like to run it locally using `cwltool`, a basic primer on that can be found [here](https://www.notion.so/d3b/Starting-From-Scratch-Running-CWLtool-b8dbbde2dc7742e4aff290b0a878344d) and combined with app-specific info from the readme below.
This workflow is the current production workflow, equivalent to this [Cavatica public app](https://cavatica.sbgenomics.com/public/apps#cavatica/apps-publisher/kfdrc-jointgenotyping-refinement-workflow).
### Runtime Estimates
- Trio of 6 GB gVCFs Input: 540 Minutes & ~$6.95
### Tips To Run:
1. inputs vcf files are the gVCF files from GATK Haplotype Caller, need to have the index **.tbi** files copy to the same project too.
1. If you are experiencing issues with Variant Recalibration either in VariantRecalibrator or ApplyVQSR, consider adjusting the max_gaussians. If a dataset gives fewer variants than the expected scale, the number of Gaussians for training should be turned down. Lowering the max-Gaussians forces the program to group variants into a smaller number of clusters, which results in more variants per cluster.
1. ped file in the input shows the family relationship between samples, the format should be the same as in GATK website [link](https://gatkforums.broadinstitute.org/gatk/discussion/7696/pedigree-ped-files), the Individual ID, Paternal ID and Maternal ID must be the same as in the inputs vcf files header.
1. Here we recommend to use GRCh38 as reference genome to do the analysis, positions in gVCF should be GRCh38 too.
1. Reference locations:
- https://console.cloud.google.com/storage/browser/genomics-public-data/resources/broad/hg38/v0/
- kfdrc bucket: s3://kids-first-seq-data/broad-references/, s3://kids-first-seq-data/pipeline-references/
- cavatica: https://cavatica.sbgenomics.com/u/kfdrc-harmonization/kf-references/
1. Suggested inputs:
- Axiom_Exome_Plus.genotypes.all_populations.poly.hg38.vcf.gz
- Homo_sapiens_assembly38.dbsnp138.vcf
- hapmap_3.3.hg38.vcf.gz
- Mills_and_1000G_gold_standard.indels.hg38.vcf.gz
- 1000G_omni2.5.hg38.vcf.gz
- 1000G_phase1.snps.high_confidence.hg38.vcf.gz
- Homo_sapiens_assembly38.dict
- Homo_sapiens_assembly38.fasta.fai
- Homo_sapiens_assembly38.fasta
- 1000G_phase3_v4_20130502.sites.hg38.vcf
- hg38.even.handcurated.20k.intervals
- homo_sapiens_merged_vep_105_GRCh38.tar.gz, from ftp://ftp.ensembl.org/pub/release-105/variation/indexed_vep_cache/ - variant effect predictor cache.
- gnomad_v3.1.1.custom.echtvar.zip
- wgs_evaluation_regions.hg38.interval_list
1. Optional inputs:
- dbNSFP4.3a_grch38.gz
- dbNSFP4.3a_grch38.gz.tbi
- dbNSFP4.3a_grch38.readme.txt
- CADDv1.6-38-gnomad.genomes.r3.0.indel.tsv.gz
- CADDv1.6-38-whole_genome_SNVs.tsv.gz
- clinvar_20220507_chr.vcf.gz
## Import info on cloning the git repo
This repo takes advantage of the git submodule feature.
The germline annotation workflow is maintained in a different repo.
Therefore, in order to get the rest of the code after cloning, you need to run: `git submodule init` and `git submodule update`.
Currently this workflow uses tools from `v1.1.0` of the annotation workflow.
If that is updated, submodule should be as well.
More info on how this works [here](https://git-scm.com/book/en/v2/Git-Tools-Submodules)
### Annotation sub workflow
Information of default annotation performed can be found in the [Kids First DRC Germline SNV Annotation Workflow docs](kf-annotation-tools/docs/GERMLINE_SNV_ANNOT_README.md)
## Other Resources
- dockerfiles: https://github.com/d3b-center/bixtools
requirements:
- class: ScatterFeatureRequirement
- class: SubworkflowFeatureRequirement
inputs:
input_vcfs: {type: 'File[]', doc: 'Input array of individual sample gVCF files'}
axiomPoly_resource_vcf: {type: File, doc: 'Axiom_Exome_Plus.genotypes.all_populations.poly.hg38.vcf.gz', "sbg:suggestedValue": {
class: File, path: 60639016357c3a53540ca7c7, name: Axiom_Exome_Plus.genotypes.all_populations.poly.hg38.vcf.gz}}
axiomPoly_resource_tbi: {type: 'File?', doc: 'Axiom_Exome_Plus.genotypes.all_populations.poly.hg38.vcf.gz.tbi', "sbg:suggestedValue": {
class: File, path: 6063901d357c3a53540ca81b, name: Axiom_Exome_Plus.genotypes.all_populations.poly.hg38.vcf.gz.tbi}}
dbsnp_vcf: {type: File, doc: 'Homo_sapiens_assembly38.dbsnp138.vcf', "sbg:suggestedValue": {class: File, path: 6063901f357c3a53540ca84b,
name: Homo_sapiens_assembly38.dbsnp138.vcf}}
dbsnp_idx: {type: 'File?', doc: 'Homo_sapiens_assembly38.dbsnp138.vcf.idx', "sbg:suggestedValue": {class: File, path: 6063901e357c3a53540ca834,
name: Homo_sapiens_assembly38.dbsnp138.vcf.idx}}
hapmap_resource_vcf: {type: File, doc: 'Hapmap genotype SNP input vcf', "sbg:suggestedValue": {class: File, path: 60639016357c3a53540ca7be,
name: hapmap_3.3.hg38.vcf.gz}}
hapmap_resource_tbi: {type: 'File?', doc: 'Hapmap genotype SNP input tbi', "sbg:suggestedValue": {class: File, path: 60639016357c3a53540ca7c5,
name: hapmap_3.3.hg38.vcf.gz.tbi}}
mills_resource_vcf: {type: File, doc: 'Mills_and_1000G_gold_standard.indels.hg38.vcf.gz', "sbg:suggestedValue": {class: File, path: 6063901a357c3a53540ca7f3,
name: Mills_and_1000G_gold_standard.indels.hg38.vcf.gz}}
mills_resource_tbi: {type: 'File?', doc: 'Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi', "sbg:suggestedValue": {class: File,
path: 6063901c357c3a53540ca806, name: Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi}}
omni_resource_vcf: {type: File, doc: '1000G_omni2.5.hg38.vcf.gz', "sbg:suggestedValue": {class: File, path: 6063901e357c3a53540ca835,
name: 1000G_omni2.5.hg38.vcf.gz}}
omni_resource_tbi: {type: 'File?', doc: '1000G_omni2.5.hg38.vcf.gz.tbi', "sbg:suggestedValue": {class: File, path: 60639016357c3a53540ca7b1,
name: 1000G_omni2.5.hg38.vcf.gz.tbi}}
one_thousand_genomes_resource_vcf: {type: File, doc: '1000G_phase1.snps.high_confidence.hg38.vcf.gz, high confidence snps', "sbg:suggestedValue": {
class: File, path: 6063901c357c3a53540ca80f, name: 1000G_phase1.snps.high_confidence.hg38.vcf.gz}}
one_thousand_genomes_resource_tbi: {type: 'File?', doc: '1000G_phase1.snps.high_confidence.hg38.vcf.gz.tbi, high confidence snps',
"sbg:suggestedValue": {class: File, path: 6063901e357c3a53540ca845, name: 1000G_phase1.snps.high_confidence.hg38.vcf.gz.tbi}}
ped: {type: File, doc: 'Ped file for the family relationship'}
reference_dict: {type: 'File?', doc: 'Homo_sapiens_assembly38.dict', "sbg:suggestedValue": {class: File, path: 60639019357c3a53540ca7e7,
name: Homo_sapiens_assembly38.dict}}
reference_fai: {type: 'File?', doc: 'Homo_sapiens_assembly38.fasta.fai', "sbg:suggestedValue": {class: File, path: 60639016357c3a53540ca7af,
name: Homo_sapiens_assembly38.fasta.fai}}
reference_fasta: {type: File, doc: 'Homo_sapiens_assembly38.fasta', "sbg:suggestedValue": {class: File, path: 60639014357c3a53540ca7a3,
name: Homo_sapiens_assembly38.fasta}}
snp_sites_vcf: {type: File, doc: '1000G_phase3_v4_20130502.sites.hg38.vcf', "sbg:suggestedValue": {class: File, path: 60639016357c3a53540ca7b5,
name: 1000G_phase3_v4_20130502.sites.hg38.vcf}}
snp_sites_idx: {type: 'File?', doc: '1000G_phase3_v4_20130502.sites.hg38.vcf.idx', "sbg:suggestedValue": {class: File, path: 6063901d357c3a53540ca819,
name: 1000G_phase3_v4_20130502.sites.hg38.vcf.idx}}
unpadded_intervals_file: {type: File, doc: 'hg38.even.handcurated.20k.intervals', "sbg:suggestedValue": {class: File, path: 5f500135e4b0370371c051b1,
name: hg38.even.handcurated.20k.intervals}}
wgs_evaluation_interval_list: {type: File, doc: 'wgs_evaluation_regions.hg38.interval_list', "sbg:suggestedValue": {class: File,
path: 60639017357c3a53540ca7d3, name: wgs_evaluation_regions.hg38.interval_list}}
snp_max_gaussians: {type: 'int?', doc: "Interger value for max gaussians in SNP VariantRecalibration. If a dataset gives fewer variants
than the expected scale, the number of Gaussians for training should be turned down. Lowering the max-Gaussians forces the program
to group variants into a smaller number of clusters, which results in more variants per cluster."}
indel_max_gaussians: {type: 'int?', doc: "Interger value for max gaussians in INDEL VariantRecalibration. If a dataset gives fewer
variants than the expected scale, the number of Gaussians for training should be turned down. Lowering the max-Gaussians forces
the program to group variants into a smaller number of clusters, which results in more variants per cluster."}
output_basename: string
tool_name: {type: 'string?', default: "multi.vqsr.filtered.denovo.vep_105", doc: "File name string suffix to use for output files"}
# Annotation
bcftools_annot_clinvar_columns: {type: 'string?', doc: "csv string of columns from annotation to port into the input vcf", default: "INFO/ALLELEID,INFO/CLNDN,INFO/CLNDNINCL,INFO/CLNDISDB,INFO/CLNDISDBINCL,INFO/CLNHGVS,INFO/CLNREVSTAT,INFO/CLNSIG,INFO/CLNSIGCONF,INFO/CLNSIGINCL,INFO/CLNVC,INFO/CLNVCSO,INFO/CLNVI"}
echtvar_anno_zips: {type: 'File[]?', doc: "Annotation ZIP files for echtvar anno", "sbg:suggestedValue": [{class: File, path: 65c64d847dab7758206248c6,
name: gnomad.v3.1.1.custom.echtvar.zip}]}
clinvar_annotation_vcf: {type: 'File?', secondaryFiles: ['.tbi'], doc: "additional bgzipped annotation vcf file"}
# VEP-specific
vep_ram: {type: 'int?', default: 32, doc: "In GB, may need to increase this value depending on the size/complexity of input"}
vep_cores: {type: 'int?', default: 36, doc: "Number of cores to use. May need to increase for really large inputs"}
vep_buffer_size: {type: 'int?', default: 100000, doc: "Increase or decrease to balance speed and memory usage"}
vep_cache: {type: 'File', doc: "tar gzipped cache from ensembl/local converted cache", "sbg:suggestedValue": {class: File, path: 6332f8e47535110eb79c794f,
name: homo_sapiens_merged_vep_105_indexed_GRCh38.tar.gz}}
dbnsfp: {type: 'File?', secondaryFiles: [.tbi, ^.readme.txt], doc: "VEP-formatted plugin file, index, and readme file containing
dbNSFP annotations"}
dbnsfp_fields: {type: 'string?', doc: "csv string with desired fields to annotate. Use ALL to grab all", default: 'SIFT4G_pred,Polyphen2_HDIV_pred,Polyphen2_HVAR_pred,LRT_pred,MutationTaster_pred,MutationAssessor_pred,FATHMM_pred,PROVEAN_pred,VEST4_score,VEST4_rankscore,MetaSVM_pred,MetaLR_pred,MetaRNN_pred,M-CAP_pred,REVEL_score,REVEL_rankscore,PrimateAI_pred,DEOGEN2_pred,BayesDel_noAF_pred,ClinPred_pred,LIST-S2_pred,Aloft_pred,fathmm-MKL_coding_pred,fathmm-XF_coding_pred,Eigen-phred_coding,Eigen-PC-phred_coding,phyloP100way_vertebrate,phyloP100way_vertebrate_rankscore,phastCons100way_vertebrate,phastCons100way_vertebrate_rankscore,TWINSUK_AC,TWINSUK_AF,ALSPAC_AC,ALSPAC_AF,UK10K_AC,UK10K_AF,gnomAD_exomes_controls_AC,gnomAD_exomes_controls_AN,gnomAD_exomes_controls_AF,gnomAD_exomes_controls_nhomalt,gnomAD_exomes_controls_POPMAX_AC,gnomAD_exomes_controls_POPMAX_AN,gnomAD_exomes_controls_POPMAX_AF,gnomAD_exomes_controls_POPMAX_nhomalt,Interpro_domain,GTEx_V8_gene,GTEx_V8_tissue'}
merged: {type: 'boolean?', doc: "Set to true if merged cache used", default: true}
cadd_indels: {type: 'File?', secondaryFiles: [.tbi], doc: "VEP-formatted plugin file and index containing CADD indel annotations"}
cadd_snvs: {type: 'File?', secondaryFiles: [.tbi], doc: "VEP-formatted plugin file and index containing CADD SNV annotations"}
intervar: {type: 'File?', doc: "Intervar vcf-formatted file. Exonic SNVs only - for more comprehensive run InterVar. See docs for
custom build instructions", secondaryFiles: [.tbi]}
outputs:
collectvariantcallingmetrics: {type: 'File[]', doc: 'Variant calling summary and detailed metrics files', outputSource: picard_collectvariantcallingmetrics/output}
peddy_html: {type: 'File[]', doc: 'html summary of peddy results', outputSource: peddy/output_html}
peddy_csv: {type: 'File[]', doc: 'csv details of peddy results', outputSource: peddy/output_csv}
peddy_ped: {type: 'File[]', doc: 'ped format summary of peddy results', outputSource: peddy/output_peddy}
cgp_vep_annotated_vcf: {type: 'File[]', outputSource: annotate_vcf/annotated_vcf}
steps:
prepare_reference:
run: ../subworkflows/prepare_reference.cwl
in:
input_fasta: reference_fasta
input_fai: reference_fai
input_dict: reference_dict
out: [indexed_fasta, reference_dict]
index_axiomPoly:
run: ../tools/tabix_index.cwl
in:
input_file: axiomPoly_resource_vcf
input_index: axiomPoly_resource_tbi
out: [output]
index_dbsnp:
run: ../tools/gatk_indexfeaturefile.cwl
in:
input_file: dbsnp_vcf
input_index: dbsnp_idx
out: [output]
index_hapmap:
run: ../tools/tabix_index.cwl
in:
input_file: hapmap_resource_vcf
input_index: hapmap_resource_tbi
out: [output]
index_mills:
run: ../tools/tabix_index.cwl
in:
input_file: mills_resource_vcf
input_index: mills_resource_tbi
out: [output]
index_omni:
run: ../tools/tabix_index.cwl
in:
input_file: omni_resource_vcf
input_index: omni_resource_tbi
out: [output]
index_1k:
run: ../tools/tabix_index.cwl
in:
input_file: one_thousand_genomes_resource_vcf
input_index: one_thousand_genomes_resource_tbi
out: [output]
index_snp:
run: ../tools/gatk_indexfeaturefile.cwl
in:
input_file: snp_sites_vcf
input_index: snp_sites_idx
out: [output]
dynamicallycombineintervals:
run: ../tools/script_dynamicallycombineintervals.cwl
label: 'Combine intervals'
doc: 'Merge interval lists based on number of gVCF inputs'
in:
input_vcfs: input_vcfs
interval: unpadded_intervals_file
out: [out_intervals]
gatk_import_genotype_filtergvcf_merge:
run: ../tools/gatk_import_genotype_filtergvcf_merge.cwl
label: 'Genotype, filter, & merge'
doc: 'Use GATK GenomicsDBImport, VariantFiltration GenotypeGVCFs, and picard MakeSitesOnlyVcf to genotype, filter and merge gVCF
based on known sites'
hints:
- class: sbg:AWSInstanceType
value: r5.4xlarge
in:
input_vcfs: input_vcfs
interval: dynamicallycombineintervals/out_intervals
dbsnp_vcf: index_dbsnp/output
reference_fasta: prepare_reference/indexed_fasta
scatter: [interval]
out: [variant_filtered_vcf, sites_only_vcf]
gatk_gathervcfs:
run: ../tools/gatk_gathervcfs.cwl
label: 'Gather VCFs'
doc: 'Merge VCFs scattered from previous step'
in:
input_vcfs: gatk_import_genotype_filtergvcf_merge/sites_only_vcf
out: [output]
gatk_snpsvariantrecalibratorcreatemodel:
run: ../tools/gatk_snpsvariantrecalibratorcreatemodel.cwl
label: 'GATK VariantRecalibrator SNPs'
doc: 'Create recalibration model for snps using GATK VariantRecalibrator, tranch values, and known site VCFs'
in:
dbsnp_resource_vcf: index_dbsnp/output
hapmap_resource_vcf: index_hapmap/output
omni_resource_vcf: index_omni/output
one_thousand_genomes_resource_vcf: index_1k/output
sites_only_variant_filtered_vcf: gatk_gathervcfs/output
max_gaussians: snp_max_gaussians
out: [model_report]
gatk_indelsvariantrecalibrator:
run: ../tools/gatk_indelsvariantrecalibrator.cwl
label: 'GATK VariantRecalibrator Indels'
doc: 'Create recalibration model for indels using GATK VariantRecalibrator, tranch values, and known site VCFs'
in:
axiomPoly_resource_vcf: index_axiomPoly/output
dbsnp_resource_vcf: index_dbsnp/output
mills_resource_vcf: index_mills/output
sites_only_variant_filtered_vcf: gatk_gathervcfs/output
max_gaussians: indel_max_gaussians
out: [recalibration, tranches]
gatk_snpsvariantrecalibratorscattered:
run: ../tools/gatk_snpsvariantrecalibratorscattered.cwl
label: 'GATK VariantRecalibrator Scatter'
doc: 'Create recalibration model for known sites from input data using GATK VariantRecalibrator, tranch values, and known site
VCFs'
hints:
- class: sbg:AWSInstanceType
value: r5.4xlarge
in:
sites_only_variant_filtered_vcf: gatk_import_genotype_filtergvcf_merge/sites_only_vcf
model_report: gatk_snpsvariantrecalibratorcreatemodel/model_report
hapmap_resource_vcf: index_hapmap/output
omni_resource_vcf: index_omni/output
one_thousand_genomes_resource_vcf: index_1k/output
dbsnp_resource_vcf: index_dbsnp/output
max_gaussians: snp_max_gaussians
scatter: [sites_only_variant_filtered_vcf]
out: [recalibration, tranches]
gatk_gathertranches:
run: ../tools/gatk_gathertranches.cwl
label: 'GATK GatherTranches'
doc: 'Gather tranches from SNP variant recalibrate scatter'
in:
tranches: gatk_snpsvariantrecalibratorscattered/tranches
out: [output]
gatk_applyrecalibration:
run: ../tools/gatk_applyrecalibration.cwl
label: 'GATK ApplyVQSR'
doc: 'Apply recalibration to snps and indels'
hints:
- class: sbg:AWSInstanceType
value: r5.4xlarge
in:
indels_recalibration: gatk_indelsvariantrecalibrator/recalibration
indels_tranches: gatk_indelsvariantrecalibrator/tranches
input_vcf: gatk_import_genotype_filtergvcf_merge/variant_filtered_vcf
snps_recalibration: gatk_snpsvariantrecalibratorscattered/recalibration
snps_tranches: gatk_gathertranches/output
scatter: [input_vcf, snps_recalibration]
scatterMethod: dotproduct
out: [recalibrated_vcf]
gatk_gatherfinalvcf:
run: ../tools/gatk_gatherfinalvcf.cwl
label: 'GATK GatherVcfsCloud'
doc: 'Combine resultant VQSR VCFs'
in:
input_vcfs: gatk_applyrecalibration/recalibrated_vcf
output_basename: output_basename
out: [output]
peddy:
run: ../tools/kfdrc_peddy_tool.cwl
label: 'Peddy'
doc: 'QC family relationships and sex assignment'
in:
ped: ped
vqsr_vcf: gatk_gatherfinalvcf/output
output_basename: output_basename
out: [output_html, output_csv, output_peddy]
picard_collectvariantcallingmetrics:
run: ../tools/picard_collectvariantcallingmetrics.cwl
label: 'CollectVariantCallingMetrics'
doc: 'picard calculate variant calling metrics'
in:
input_vcf: gatk_gatherfinalvcf/output
reference_dict: prepare_reference/reference_dict
output_basename: output_basename
dbsnp_vcf: index_dbsnp/output
wgs_evaluation_interval_list: wgs_evaluation_interval_list
out: [output]
gatk_calculategenotypeposteriors:
in:
ped: ped
reference_fasta: prepare_reference/indexed_fasta
snp_sites: index_snp/output
vqsr_vcf: gatk_gatherfinalvcf/output
output_basename: output_basename
out: [output]
run: ../tools/gatk_calculategenotypeposteriors.cwl
gatk_variantfiltration:
in:
cgp_vcf: gatk_calculategenotypeposteriors/output
reference_fasta: prepare_reference/indexed_fasta
output_basename: output_basename
out: [output]
run: ../tools/gatk_variantfiltration.cwl
gatk_variantannotator:
in:
cgp_filtered_vcf: gatk_variantfiltration/output
ped: ped
reference_fasta: prepare_reference/indexed_fasta
output_basename: output_basename
out: [output]
run: ../tools/gatk_variantannotator.cwl
annotate_vcf:
run: ../kf-annotation-tools/workflows/kfdrc-germline-snv-annot-workflow.cwl
in:
indexed_reference_fasta: prepare_reference/indexed_fasta
input_vcf: gatk_variantannotator/output
output_basename: output_basename
tool_name: tool_name
bcftools_annot_clinvar_columns: bcftools_annot_clinvar_columns
echtvar_anno_zips: echtvar_anno_zips
clinvar_annotation_vcf: clinvar_annotation_vcf
vep_ram: vep_ram
vep_cores: vep_cores
vep_buffer_size: vep_buffer_size
vep_cache: vep_cache
dbnsfp: dbnsfp
dbnsfp_fields: dbnsfp_fields
cadd_indels: cadd_indels
cadd_snvs: cadd_snvs
merged: merged
intervar: intervar
out: [annotated_vcf]
$namespaces:
sbg: https://sevenbridges.com
hints:
- class: sbg:maxNumberOfParallelInstances
value: 2
"sbg:license": Apache License 2.0
"sbg:publisher": KFDRC
"sbg:categories":
- GATK
- GENOTYPING
- JOINT
- PEDDY
- VCF
- VEP
"sbg:links":
- id: 'https://github.com/kids-first/kf-jointgenotyping-workflow/releases/tag/v2.4.0'
label: github-release