Genomic variants - SNPs and INDELs detection using VARSCAN2.

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Author: AMBARISH KUMAR er.ambarish@gmail.com ; ambari73_sit@jnu.ac.in

This is a proposed standard operating procedure for genomic variant detection using VARSCAN.

It is hoped to be effective and useful for getting SARS-CoV-2 genome variants.

It uses Illumina RNASEQ reads and genome sequence.

Code Snippets

baseCommand:
  - bowtie2

arguments:
  - valueFrom: |
      ${
        if (inputs.filelist && inputs.filelist_mates){
          return "-1";
        } else if (inputs.filelist){
          return "-U";
        } else {
          return null;
        }
      }
    position: 82
  - valueFrom: |
      ${
        if (inputs.filelist && inputs.filelist_mates){
          return "-2";
        } else if (inputs.filelist_mates){
          return "-U";
        } else {
          return null;
        }
      }
    position: 84
  - valueFrom: |
      ${
        if (inputs.output_filename == ""){
          return ' 2> ' + default_output_filename().split('.').slice(0,-1).join('.') + '.log';
        } else {
          return ' 2> ' + inputs.output_filename.split('.').slice(0,-1).join('.') + '.log';
        }
      }
    position: 100000
    shellQuote: false

CWL Bowtie 2 From line 864 of release/bowtie2_align.cwl

baseCommand:
  - bowtie2-build

arguments:
  - valueFrom: $('2> ' + inputs.bt2_index_base + '.log')
    position: 100000
    shellQuote: false

CWL Bowtie 2 From line 226 of release/bowtie2_build.cwl

baseCommand: []
arguments:
- valueFrom: varscan mpileup2indel $(inputs.inputMpileup.path) > $(inputs.sampleName).indel.vcf
  shellQuote: false

CWL VarScan From line 25 of release/mpileup2indel.cwl

baseCommand: []
arguments:
- valueFrom: varscan mpileup2snp $(inputs.inputMpileup.path) > $(inputs.sampleName).snp.vcf
  shellQuote: false

CWL VarScan From line 25 of release/mpileup2snp.cwl

baseCommand: [ samtools, faidx ]

inputs:
  sequences:
    type: File
    doc: Input FASTA file


arguments:
   - $(inputs.sequences.basename)

CWL From line 12 of release/samtools_faidx.cwl

baseCommand: ["samtools", "index"]
arguments:
  - valueFrom: -b  # specifies that index is created in bai format
    position: 1

inputs:
  bam_sorted:
    doc: sorted bam input file
    type: File
    inputBinding:
      position: 2

CWL SAMtools From line 19 of release/samtools_index.cwl

baseCommand: []
arguments:
- valueFrom: |-
    samtools index $(inputs.inputBAM.path) | samtools mpileup -B -f $(inputs.ReferenceGenome.path) $(inputs.inputBAM.path) > $(inputs.sampleName).mpileup
  shellQuote: false

CWL SAMtools From line 41 of release/samtools_mpileup.cwl

baseCommand: ["samtools", "sort"]

inputs:
  bam_unsorted:
    doc: aligned reads to be checked in sam or bam format
    type: File
    inputBinding:
      position: 2
  by_name:
    doc: If true, will sort by name, otherwise will sort by genomic position
    type: boolean
    default: false
    inputBinding:
      position: 1
      prefix: -n

CWL SAMtools From line 14 of release/samtools_sort.cwl

baseCommand: ["samtools", "view"]
arguments:
  - valueFrom: -h
    position: 1
    # include the headers
  - valueFrom: -b
    position: 1
    # output in bam format