prenderj/variant_tutorial

Course material for the genetic variant calling tutorial at ILRI Ethiopia **The slides accompanying this tutorial can be found here** # Table of contents Session 1: Variant calling with GATK Session 2: Variant annotation and filtering Session 3: Association study with plink # Session 1: Variant calling with GATK ## Dataset After starting the interactive session the data you need for this session can be copied from */export/data/ilri/bioinformatics/workshop_dnaseq/Session1*. ``` interactive -c 4 ``` We first go to the home directory, then copy the required data and move to this new directory ``` cd cp -R /export/data/ilri/bioinformatics/workshop_dnaseq/Session1/ ~/ cd ~/Session1 ``` This session will take you through the process of calling variants with GATK using cattle whole genome sequencing data. There are 2 bam files in the Session1 folder you just copied (aligned with BWA), each corresponding to a different cow. These contain reads mapping to an approximately 4Mb region centred on the cow Leptin gene on chromosome 4 (you can view the region here: ensembl.org). Programs required: * R (cran.r-project.org) * Samtools (htslib.org) * Picard (broadinstitute.github.io) * GATK (software.broadinstitute.org) * VCFtools (vcftools.github.io) These are already installed on the ILRI cluster. To make them available type: ``` module load samtools/1.3.1 module load picard/2.8.2 module load gatk/3.7.0 module load R/3.6 module load vcftools/0.1.15 ``` ## 1. Preparing the reference genome for use with GATK Earlier we showed you how to map your reads against a reference genome, and these bams were aligned with BWA. To run GATK it is first necessary to create partner files to the fasta format reference genome used to do the alignment; a fasta index file (.fai) and a dictionary file (.dict). We have provided the reference genome used to align these data (Bos_taurus.UMD3.1.dna.toplevel.fa). The par …