GATK Base Recalibration on Bam¶

GATKBaseRecalBQSRWorkflow · 1 contributor · 2 versions

No documentation was provided: contribute one

Quickstart¶

from janis_bioinformatics.tools.common.gatkbasecalbam import GATKBaseRecalBQSRWorkflow_4_1_3

wf = WorkflowBuilder("myworkflow")

wf.step(
    "gatkbaserecalbqsrworkflow_step",
    GATKBaseRecalBQSRWorkflow_4_1_3(
        bam=None,
        reference=None,
        snps_dbsnp=None,
        snps_1000gp=None,
        known_indels=None,
        mills_indels=None,
    )
)
wf.output("out", source=gatkbaserecalbqsrworkflow_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 GATKBaseRecalBQSRWorkflow:

# user inputs
janis inputs GATKBaseRecalBQSRWorkflow > inputs.yaml

inputs.yaml

bam: bam.bam
known_indels: known_indels.vcf.gz
mills_indels: mills_indels.vcf.gz
reference: reference.fasta
snps_1000gp: snps_1000gp.vcf.gz
snps_dbsnp: snps_dbsnp.vcf.gz

Run GATKBaseRecalBQSRWorkflow with:

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

Information¶

URL: No URL to the documentation was provided

ID:	`GATKBaseRecalBQSRWorkflow`
URL:	No URL to the documentation was provided
Versions:	4.1.2, 4.1.3
Authors:	Jiaan Yu
Citations:
Created:	2020-06-12
Updated:	2020-06-12

Outputs¶

name	type	documentation
out	IndexedBam

Workflow¶

Embedded Tools¶

GATK4: Base Recalibrator	`Gatk4BaseRecalibrator/4.1.3.0`
GATK4: Apply base quality score recalibration	`Gatk4ApplyBQSR/4.1.3.0`

Additional configuration (inputs)¶

name	type	documentation
bam	IndexedBam
reference	FastaWithIndexes
snps_dbsnp	Gzipped<VCF>
snps_1000gp	Gzipped<VCF>
known_indels	Gzipped<VCF>
mills_indels	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

Workflow Description Language¶

version development

import "tools/Gatk4BaseRecalibrator_4_1_3_0.wdl" as G
import "tools/Gatk4ApplyBQSR_4_1_3_0.wdl" as G2

workflow GATKBaseRecalBQSRWorkflow {
  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 snps_dbsnp
    File snps_dbsnp_tbi
    File snps_1000gp
    File snps_1000gp_tbi
    File known_indels
    File known_indels_tbi
    File mills_indels
    File mills_indels_tbi
  }
  call G.Gatk4BaseRecalibrator as base_recalibrator {
    input:
      bam=bam,
      bam_bai=bam_bai,
      knownSites=[snps_dbsnp, snps_1000gp, known_indels, mills_indels],
      knownSites_tbi=[snps_dbsnp_tbi, snps_1000gp_tbi, known_indels_tbi, mills_indels_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,
      intervals=intervals
  }
  call G2.Gatk4ApplyBQSR as apply_bqsr {
    input:
      bam=bam,
      bam_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,
      recalFile=base_recalibrator.out,
      intervals=intervals
  }
  output {
    File out = apply_bqsr.out
    File out_bai = apply_bqsr.out_bai
  }
}

Common Workflow Language¶

#!/usr/bin/env cwl-runner
class: Workflow
cwlVersion: v1.2
label: GATK Base Recalibration on Bam
doc: ''

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: snps_dbsnp
  type: File
  secondaryFiles:
  - pattern: .tbi
- id: snps_1000gp
  type: File
  secondaryFiles:
  - pattern: .tbi
- id: known_indels
  type: File
  secondaryFiles:
  - pattern: .tbi
- id: mills_indels
  type: File
  secondaryFiles:
  - pattern: .tbi

outputs:
- id: out
  type: File
  secondaryFiles:
  - pattern: .bai
  outputSource: apply_bqsr/out

steps:
- id: base_recalibrator
  label: 'GATK4: Base Recalibrator'
  in:
  - id: bam
    source: bam
  - id: knownSites
    source:
    - snps_dbsnp
    - snps_1000gp
    - known_indels
    - mills_indels
  - id: reference
    source: reference
  - id: intervals
    source: intervals
  run: tools/Gatk4BaseRecalibrator_4_1_3_0.cwl
  out:
  - id: out
- id: apply_bqsr
  label: 'GATK4: Apply base quality score recalibration'
  in:
  - id: bam
    source: bam
  - id: reference
    source: reference
  - id: recalFile
    source: base_recalibrator/out
  - id: intervals
    source: intervals
  run: tools/Gatk4ApplyBQSR_4_1_3_0.cwl
  out:
  - id: out
id: GATKBaseRecalBQSRWorkflow