<![CDATA[BOL: Variant Calling Pipeline]]> https://bioinformaticsonline.com/bookmarks/view/44675/variant-calling-pipeline? https://bioinformaticsonline.com/bookmarks/view/44675/variant-calling-pipeline Sat, 19 Oct 2024 12:23:40 -0500 https://bioinformaticsonline.com/bookmarks/view/44675/variant-calling-pipeline <![CDATA[Variant Calling Pipeline]]> The variantcalling.nf nextflow script will take any number of samples with paired-end reads in FASTQ format, map reads using Bowtie2, process BAM files, and finally call variants using BCFtools v1.21 and/or Freebayes v1.3.6. If part of the pipeline is unsuccessful for a sample then these errors are ignored.

Pipeline flowchart:

 
 

Dependencies (version tested)

  • Nextflow (24.04.4)
  • Java (18.0.2.1)
  • Python (3.10)
  • Perl (5.32.1)
  • Bowtie2 (2.5.3)
  • SAMtools (1.19.2)
  • GATK4 (4.5)
  • BCFtools (1.21)
  • Freebayes (1.3.6)

Address of the bookmark: https://github.com/Tom-Jenkins/nextflow-pipelines/blob/main/docs/variant-calling.md

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