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
Go here for usage.
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