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

This repository contains workflows/pipelines for the following tasks:

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

It takes as input FASTQ or BAM files which are specified in the nextflow.config file.

Basic Usage

• Get reads quality reports

$ nextflow run getFastqBamQualityReports.nf -w /path/to/work-directory/ -profile local

• Align reads to reference

$ nextflow run alignReadsToReference.nf -w /path/to/work-directory/ -profile chpc

• Call variants from aligned BAM files

$ nextflow run callVariants.nf -w /path/to/work-directory/ -profile ucthpc

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