/genemapngs

Workflows for whole-genome/exome sequencing data analysis

Primary LanguageNextflowGNU General Public License v3.0GPL-3.0

READS QUALITY, ALIGNMENT, VARIANT CALLING, VARIANT FILTERING, AND ANNOTATION WORKFLOW

This repository contains workflows/pipelines for the following tasks:

  • Reads quality assessment: getQualityReports.nf
  • Reads alignment to reference: alignReadsToReference.nf
  • Variant calling: callVariants.nf
  • Variant fltering: filterVariantCalls.nf
  • Variant annotation: annotateVariants.nf

Documentation

Go here for usage.

IMPORTANT NOTE

You must build the indices of all references in the same directory as the references for this workflow to run successfully

  • Build BWA index
$ bwa index ref
  • Build GATK index
$ gatk CreateSequenceDictionary -R ref
  • Build .fai index with SAMTOOLS FAIDX
$ samtools faidx ref