Strelka Somatic Variant Caller¶

strelkaSomaticVariantCaller · 2 contributors · 1 version

No documentation was provided: contribute one

Quickstart¶

from janis_bioinformatics.tools.variantcallers.illuminasomatic_strelka import IlluminaSomaticVariantCaller

wf = WorkflowBuilder("myworkflow")

wf.step(
    "strelkasomaticvariantcaller_step",
    IlluminaSomaticVariantCaller(
        normal_bam=None,
        tumor_bam=None,
        reference=None,
    )
)
wf.output("sv", source=strelkasomaticvariantcaller_step.sv)
wf.output("variants", source=strelkasomaticvariantcaller_step.variants)
wf.output("out", source=strelkasomaticvariantcaller_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 strelkaSomaticVariantCaller:

# user inputs
janis inputs strelkaSomaticVariantCaller > inputs.yaml

inputs.yaml

normal_bam: normal_bam.bam
reference: reference.fasta
tumor_bam: tumor_bam.bam

Run strelkaSomaticVariantCaller with:

janis run [...run options] \
    --inputs inputs.yaml \
    strelkaSomaticVariantCaller

Information¶

URL: No URL to the documentation was provided

ID:	`strelkaSomaticVariantCaller`
URL:	No URL to the documentation was provided
Versions:	v0.1.1
Authors:	Jiaan Yu, Michael Franklin
Citations:
Created:	2020-06-12
Updated:	2020-08-25

Outputs¶

name	type	documentation
sv	Gzipped<VCF>
variants	Gzipped<VCF>
out	VCF

Workflow¶

../../../_images/strelkaSomaticVariantCaller_v0_1_1.dot.png

Embedded Tools¶

Manta	`manta/1.5.0`
Strelka (Somatic)	`strelka_somatic/2.9.10`
Concat Strelka Somatic Vcf	`ConcatStrelkaSomaticVcf/0.1.16`
BCFTools: Sort	`bcftoolssort/v1.9`
Split Multiple Alleles	`SplitMultiAllele/v0.5772`
Extract Strelka Somatic AD DP	`extractStrelkaSomaticADDP/0.1.1`
VcfTools	`VcfTools/0.1.16`

Additional configuration (inputs)¶

name	type	documentation
normal_bam	IndexedBam
tumor_bam	IndexedBam
reference	FastaWithIndexes
intervals	Optional<Gzipped<bed>>
is_exome	Optional<Boolean>
filterpass_removeFileteredAll	Optional<Boolean>	Removes all sites with a FILTER flag other than PASS.
filterpass_recode	Optional<Boolean>
filterpass_recodeINFOAll	Optional<Boolean>	These options can be used with the above recode options to define an INFO key name to keep in the output file. This option can be used multiple times to keep more of the INFO fields. The second option is used to keep all INFO values in the original file.

Workflow Description Language¶

version development

import "tools/manta_1_5_0.wdl" as M
import "tools/strelka_somatic_2_9_10.wdl" as S
import "tools/ConcatStrelkaSomaticVcf_0_1_16.wdl" as C
import "tools/bcftoolssort_v1_9.wdl" as B
import "tools/SplitMultiAllele_v0_5772.wdl" as S2
import "tools/extractStrelkaSomaticADDP_0_1_1.wdl" as E
import "tools/VcfTools_0_1_16.wdl" as V

workflow strelkaSomaticVariantCaller {
  input {
    File normal_bam
    File normal_bam_bai
    File tumor_bam
    File tumor_bam_bai
    File reference
    File reference_fai
    File reference_amb
    File reference_ann
    File reference_bwt
    File reference_pac
    File reference_sa
    File reference_dict
    File? intervals
    File? intervals_tbi
    Boolean? is_exome
    Boolean? filterpass_removeFileteredAll = true
    Boolean? filterpass_recode = true
    Boolean? filterpass_recodeINFOAll = true
  }
  call M.manta as manta {
    input:
      bam=normal_bam,
      bam_bai=normal_bam_bai,
      reference=reference,
      reference_fai=reference_fai,
      tumorBam=tumor_bam,
      tumorBam_bai=tumor_bam_bai,
      exome=is_exome,
      callRegions=intervals,
      callRegions_tbi=intervals_tbi
  }
  call S.strelka_somatic as strelka {
    input:
      normalBam=normal_bam,
      normalBam_bai=normal_bam_bai,
      tumorBam=tumor_bam,
      tumorBam_bai=tumor_bam_bai,
      reference=reference,
      reference_fai=reference_fai,
      indelCandidates=[manta.candidateSmallIndels],
      indelCandidates_tbi=[manta.candidateSmallIndels_tbi],
      exome=is_exome,
      callRegions=intervals,
      callRegions_tbi=intervals_tbi
  }
  call C.ConcatStrelkaSomaticVcf as concatvcf {
    input:
      headerVcfs=[strelka.snvs, strelka.indels],
      headerVcfs_tbi=[strelka.snvs_tbi, strelka.indels_tbi],
      contentVcfs=[strelka.snvs, strelka.indels],
      contentVcfs_tbi=[strelka.snvs_tbi, strelka.indels_tbi]
  }
  call B.bcftoolssort as sortvcf {
    input:
      vcf=concatvcf.out
  }
  call S2.SplitMultiAllele as splitnormalisevcf {
    input:
      vcf=sortvcf.out,
      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 E.extractStrelkaSomaticADDP as extractaddp {
    input:
      vcf=splitnormalisevcf.out
  }
  call V.VcfTools as filterpass {
    input:
      vcf=extractaddp.out,
      removeFileteredAll=select_first([filterpass_removeFileteredAll, true]),
      recode=select_first([filterpass_recode, true]),
      recodeINFOAll=select_first([filterpass_recodeINFOAll, true])
  }
  output {
    File sv = manta.diploidSV
    File sv_tbi = manta.diploidSV_tbi
    File variants = sortvcf.out
    File out = filterpass.out
  }
}

Common Workflow Language¶

#!/usr/bin/env cwl-runner
class: Workflow
cwlVersion: v1.2
label: Strelka Somatic Variant Caller
doc: ''

requirements:
- class: InlineJavascriptRequirement
- class: StepInputExpressionRequirement
- class: MultipleInputFeatureRequirement

inputs:
- id: normal_bam
  type: File
  secondaryFiles:
  - pattern: .bai
- id: tumor_bam
  type: File
  secondaryFiles:
  - pattern: .bai
- id: reference
  type: File
  secondaryFiles:
  - pattern: .fai
  - pattern: .amb
  - pattern: .ann
  - pattern: .bwt
  - pattern: .pac
  - pattern: .sa
  - pattern: ^.dict
- id: intervals
  type:
  - File
  - 'null'
  secondaryFiles:
  - pattern: .tbi
- id: is_exome
  type:
  - boolean
  - 'null'
- id: filterpass_removeFileteredAll
  doc: Removes all sites with a FILTER flag other than PASS.
  type: boolean
  default: true
- id: filterpass_recode
  doc: ''
  type: boolean
  default: true
- id: filterpass_recodeINFOAll
  doc: |-
    These options can be used with the above recode options to define an INFO key name to keep in the output  file.  This  option can be used multiple times to keep more of the INFO fields. The second option is used to keep all INFO values in the original file.
  type: boolean
  default: true

outputs:
- id: sv
  type: File
  secondaryFiles:
  - pattern: .tbi
  outputSource: manta/diploidSV
- id: variants
  type: File
  outputSource: sortvcf/out
- id: out
  type: File
  outputSource: filterpass/out

steps:
- id: manta
  label: Manta
  in:
  - id: bam
    source: normal_bam
  - id: reference
    source: reference
  - id: tumorBam
    source: tumor_bam
  - id: exome
    source: is_exome
  - id: callRegions
    source: intervals
  run: tools/manta_1_5_0.cwl
  out:
  - id: python
  - id: pickle
  - id: candidateSV
  - id: candidateSmallIndels
  - id: diploidSV
  - id: alignmentStatsSummary
  - id: svCandidateGenerationStats
  - id: svLocusGraphStats
  - id: somaticSVs
- id: strelka
  label: Strelka (Somatic)
  in:
  - id: normalBam
    source: normal_bam
  - id: tumorBam
    source: tumor_bam
  - id: reference
    source: reference
  - id: indelCandidates
    source:
    - manta/candidateSmallIndels
    linkMerge: merge_nested
  - id: exome
    source: is_exome
  - id: callRegions
    source: intervals
  run: tools/strelka_somatic_2_9_10.cwl
  out:
  - id: configPickle
  - id: script
  - id: stats
  - id: indels
  - id: snvs
- id: concatvcf
  label: Concat Strelka Somatic Vcf
  in:
  - id: headerVcfs
    source:
    - strelka/snvs
    - strelka/indels
  - id: contentVcfs
    source:
    - strelka/snvs
    - strelka/indels
  run: tools/ConcatStrelkaSomaticVcf_0_1_16.cwl
  out:
  - id: out
- id: sortvcf
  label: 'BCFTools: Sort'
  in:
  - id: vcf
    source: concatvcf/out
  run: tools/bcftoolssort_v1_9.cwl
  out:
  - id: out
- id: splitnormalisevcf
  label: Split Multiple Alleles
  in:
  - id: vcf
    source: sortvcf/out
  - id: reference
    source: reference
  run: tools/SplitMultiAllele_v0_5772.cwl
  out:
  - id: out
- id: extractaddp
  label: Extract Strelka Somatic AD DP
  in:
  - id: vcf
    source: splitnormalisevcf/out
  run: tools/extractStrelkaSomaticADDP_0_1_1.cwl
  out:
  - id: out
- id: filterpass
  label: VcfTools
  in:
  - id: vcf
    source: extractaddp/out
  - id: removeFileteredAll
    source: filterpass_removeFileteredAll
  - id: recode
    source: filterpass_recode
  - id: recodeINFOAll
    source: filterpass_recodeINFOAll
  run: tools/VcfTools_0_1_16.cwl
  out:
  - id: out
id: strelkaSomaticVariantCaller