GATK4 Somatic Variant Caller for Tumour Only Samples with Targeted BED¶
GATK4_SomaticVariantCallerTumorOnlyTargeted · 2 contributors · 1 version
This is a VariantCaller based on the GATK Best Practice pipelines. It uses the GATK4 toolkit, specifically 4.1.2.
It has the following steps:
- Mutect2 (output: vcf, bam, f1r2.tar.gz)
- LearnOrientationModel
- GetPileupSummaries
- CalculateContamination
- FilterMutect2Calls
- SplitNormaliseVcf
Quickstart¶
from janis_bioinformatics.tools.variantcallers.gatk.gatksomatic_variants_single import GatkSomaticVariantCallerTumorOnlyTargeted wf = WorkflowBuilder("myworkflow") wf.step( "gatk4_somaticvariantcallertumoronlytargeted_step", GatkSomaticVariantCallerTumorOnlyTargeted( bam=None, reference=None, gnomad=None, ) ) wf.output("variants", source=gatk4_somaticvariantcallertumoronlytargeted_step.variants) wf.output("out_bam", source=gatk4_somaticvariantcallertumoronlytargeted_step.out_bam) wf.output("out", source=gatk4_somaticvariantcallertumoronlytargeted_step.out)
OR
- Install Janis
- Ensure Janis is configured to work with Docker or Singularity.
- Ensure all reference files are available:
Note
More information about these inputs are available below.
- Generate user input files for GATK4_SomaticVariantCallerTumorOnlyTargeted:
# user inputs
janis inputs GATK4_SomaticVariantCallerTumorOnlyTargeted > inputs.yaml
inputs.yaml
bam: bam.bam
gnomad: gnomad.vcf.gz
reference: reference.fasta
- Run GATK4_SomaticVariantCallerTumorOnlyTargeted with:
janis run [...run options] \
--inputs inputs.yaml \
GATK4_SomaticVariantCallerTumorOnlyTargeted
Information¶
URL: No URL to the documentation was provided
| ID: | GATK4_SomaticVariantCallerTumorOnlyTargeted |
|---|---|
| URL: | No URL to the documentation was provided |
| Versions: | v0.1.1 |
| Authors: | Michael Franklin, Jiaan Yu |
| Citations: | |
| Created: | 2020-06-04 |
| Updated: | 2020-06-04 |
Outputs¶
| name | type | documentation |
|---|---|---|
| variants | Gzipped<VCF> | |
| out_bam | Optional<IndexedBam> | |
| out | VCF |
Workflow¶
Embedded Tools¶
| GatkMutect2 | Gatk4Mutect2/4.1.2.0 |
| GATK4: LearnReadOrientationModel | Gatk4LearnReadOrientationModel/4.1.2.0 |
| GATK4: GetPileupSummaries | Gatk4GetPileupSummaries/4.1.2.0 |
| GATK4: CalculateContamination | Gatk4CalculateContamination/4.1.2.0 |
| GATK4: GetFilterMutectCalls | Gatk4FilterMutectCalls/4.1.2.0 |
| Split Multiple Alleles and Normalise Vcf | SplitMultiAlleleNormaliseVcf/v0.5772 |
Additional configuration (inputs)¶
| name | type | documentation |
|---|---|---|
| bam | IndexedBam | |
| reference | FastaWithIndexes | |
| gnomad | Gzipped<VCF> | |
| intervals | Optional<bed> | This optional interval supports processing by regions. If this input resolves to null, then GATK will process the whole genome per each tool’s spec |
| panel_of_normals | Optional<Gzipped<VCF>> |
Workflow Description Language¶
version development
import "tools/Gatk4Mutect2_4_1_2_0.wdl" as G
import "tools/Gatk4LearnReadOrientationModel_4_1_2_0.wdl" as G2
import "tools/Gatk4GetPileupSummaries_4_1_2_0.wdl" as G3
import "tools/Gatk4CalculateContamination_4_1_2_0.wdl" as G4
import "tools/Gatk4FilterMutectCalls_4_1_2_0.wdl" as G5
import "tools/SplitMultiAlleleNormaliseVcf_v0_5772.wdl" as S
workflow GATK4_SomaticVariantCallerTumorOnlyTargeted {
input {
File bam
File bam_bai
File? intervals
File reference
File reference_fai
File reference_amb
File reference_ann
File reference_bwt
File reference_pac
File reference_sa
File reference_dict
File gnomad
File gnomad_tbi
File? panel_of_normals
File? panel_of_normals_tbi
}
call G.Gatk4Mutect2 as mutect2 {
input:
tumorBams=[bam],
tumorBams_bai=[bam_bai],
reference=reference,
reference_fai=reference_fai,
reference_amb=reference_amb,
reference_ann=reference_ann,
reference_bwt=reference_bwt,
reference_pac=reference_pac,
reference_sa=reference_sa,
reference_dict=reference_dict,
germlineResource=gnomad,
germlineResource_tbi=gnomad_tbi,
intervals=intervals,
panelOfNormals=panel_of_normals,
panelOfNormals_tbi=panel_of_normals_tbi
}
call G2.Gatk4LearnReadOrientationModel as learnorientationmodel {
input:
f1r2CountsFiles=[mutect2.f1f2r_out]
}
call G3.Gatk4GetPileupSummaries as getpileupsummaries {
input:
bam=[bam],
bam_bai=[bam_bai],
sites=gnomad,
sites_tbi=gnomad_tbi,
intervals=intervals
}
call G4.Gatk4CalculateContamination as calculatecontamination {
input:
pileupTable=getpileupsummaries.out
}
call G5.Gatk4FilterMutectCalls as filtermutect2calls {
input:
contaminationTable=calculatecontamination.contOut,
segmentationFile=calculatecontamination.segOut,
statsFile=mutect2.stats,
readOrientationModel=learnorientationmodel.out,
vcf=mutect2.out,
vcf_tbi=mutect2.out_tbi,
reference=reference,
reference_fai=reference_fai,
reference_amb=reference_amb,
reference_ann=reference_ann,
reference_bwt=reference_bwt,
reference_pac=reference_pac,
reference_sa=reference_sa,
reference_dict=reference_dict
}
call S.SplitMultiAlleleNormaliseVcf as splitnormalisevcf {
input:
compressedTabixVcf=filtermutect2calls.out,
compressedTabixVcf_tbi=filtermutect2calls.out_tbi,
reference=reference,
reference_fai=reference_fai,
reference_amb=reference_amb,
reference_ann=reference_ann,
reference_bwt=reference_bwt,
reference_pac=reference_pac,
reference_sa=reference_sa,
reference_dict=reference_dict
}
output {
File variants = mutect2.out
File variants_tbi = mutect2.out_tbi
File? out_bam = mutect2.bam
File? out_bam_bai = mutect2.bam_bai
File out = splitnormalisevcf.out
}
}
Common Workflow Language¶
#!/usr/bin/env cwl-runner
class: Workflow
cwlVersion: v1.2
label: GATK4 Somatic Variant Caller for Tumour Only Samples with Targeted BED
doc: |-
This is a VariantCaller based on the GATK Best Practice pipelines. It uses the GATK4 toolkit, specifically 4.1.2.
It has the following steps:
1. Mutect2 (output: vcf, bam, f1r2.tar.gz)
2. LearnOrientationModel
3. GetPileupSummaries
4. CalculateContamination
5. FilterMutect2Calls
6. SplitNormaliseVcf
requirements:
- class: InlineJavascriptRequirement
- class: StepInputExpressionRequirement
- class: MultipleInputFeatureRequirement
inputs:
- id: bam
type: File
secondaryFiles:
- pattern: .bai
- id: intervals
doc: |-
This optional interval supports processing by regions. If this input resolves to null, then GATK will process the whole genome per each tool's spec
type:
- File
- 'null'
- id: reference
type: File
secondaryFiles:
- pattern: .fai
- pattern: .amb
- pattern: .ann
- pattern: .bwt
- pattern: .pac
- pattern: .sa
- pattern: ^.dict
- id: gnomad
type: File
secondaryFiles:
- pattern: .tbi
- id: panel_of_normals
type:
- File
- 'null'
secondaryFiles:
- pattern: .tbi
outputs:
- id: variants
type: File
secondaryFiles:
- pattern: .tbi
outputSource: mutect2/out
- id: out_bam
type:
- File
- 'null'
secondaryFiles:
- pattern: .bai
outputSource: mutect2/bam
- id: out
type: File
outputSource: splitnormalisevcf/out
steps:
- id: mutect2
label: GatkMutect2
in:
- id: tumorBams
source:
- bam
linkMerge: merge_nested
- id: reference
source: reference
- id: germlineResource
source: gnomad
- id: intervals
source: intervals
- id: panelOfNormals
source: panel_of_normals
run: tools/Gatk4Mutect2_4_1_2_0.cwl
out:
- id: out
- id: stats
- id: f1f2r_out
- id: bam
- id: learnorientationmodel
label: 'GATK4: LearnReadOrientationModel'
in:
- id: f1r2CountsFiles
source:
- mutect2/f1f2r_out
linkMerge: merge_nested
run: tools/Gatk4LearnReadOrientationModel_4_1_2_0.cwl
out:
- id: out
- id: getpileupsummaries
label: 'GATK4: GetPileupSummaries'
in:
- id: bam
source:
- bam
linkMerge: merge_nested
- id: sites
source: gnomad
- id: intervals
source: intervals
run: tools/Gatk4GetPileupSummaries_4_1_2_0.cwl
out:
- id: out
- id: calculatecontamination
label: 'GATK4: CalculateContamination'
in:
- id: pileupTable
source: getpileupsummaries/out
run: tools/Gatk4CalculateContamination_4_1_2_0.cwl
out:
- id: contOut
- id: segOut
- id: filtermutect2calls
label: 'GATK4: GetFilterMutectCalls'
in:
- id: contaminationTable
source: calculatecontamination/contOut
- id: segmentationFile
source: calculatecontamination/segOut
- id: statsFile
source: mutect2/stats
- id: readOrientationModel
source: learnorientationmodel/out
- id: vcf
source: mutect2/out
- id: reference
source: reference
run: tools/Gatk4FilterMutectCalls_4_1_2_0.cwl
out:
- id: out
- id: splitnormalisevcf
label: Split Multiple Alleles and Normalise Vcf
in:
- id: compressedTabixVcf
source: filtermutect2calls/out
- id: reference
source: reference
run: tools/SplitMultiAlleleNormaliseVcf_v0_5772.cwl
out:
- id: out
id: GATK4_SomaticVariantCallerTumorOnlyTargeted