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