SNPs and INDELs detection using SAMTools.

public public 1yr ago Version: Version 1 0 bookmarks
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snps-and-indels-detection-using-samtools
snps-and-indels-detection-using-samtools
snps-and-indels-detection-using-samtools
snps-and-indels-detection-using-samtools
snps-and-indels-detection-using-samtools
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Author: AMBARISH KUMAR [email protected] ; [email protected]

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

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

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baseCommand: [ samtools, faidx ]

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


arguments:
   - $(inputs.sequences.basename)
CWL From line 12 of release/samtools_faidx.cwl 
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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 
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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 
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baseCommand: ["samtools", "view"]
arguments:
  - valueFrom: -h
    position: 1
    # include the headers
  - valueFrom: -b
    position: 1
    # output in bam format
CWL SAMtools From line 15 of release/samtools_view_sam2bam.cwl
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Created: 1yr ago
Updated: 1yr ago
Maitainers: public
URL: https://github.com/ambarishK/bio-cwl-tools/blob/release/samtoolsW.cwl
Name: snps-and-indels-detection-using-samtools
Version: Version 1
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Downloaded: 0
Copyright: Public Domain
License: Apache License 2.0
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