BioMonth - CSC supercomputing and data management for bioscientists

Description

GATK: GATK4 toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. The content on this page is borrowed from GATK webpages/courses. To get familiar with GATK tools, you can read the following:

• Read overview of GATK4 here
• Quick start guide here
• Best Practices workflows here

Download GATK container from Dockerhub

docker pull broadinstitute/gatk:latest

or with some specific-version information
docker pull broadinstitute/gatk:4.0.11.0

Start up the GATK container

docker run -it broadinstitute/gatk:latest

Run a GATK command in the container

./gatk --list

The general format for GATK commands is

gatk ToolName [tool args]

exit from the container

ctrl+p then ctrl+q

Download example data

You can download toy example dataset from CSC’s allas objects storage:

wget https://a3s.fi/Softwares/data.zip

Start running gatk container and mount the location of the data bundle inside the docker

docker run -v /path/data:/gatk/data -it broadinstitute/gatk:latest

Get usage information of HaplotypeCaller from GATK

gatk HaplotypeCaller --help

Run HaplotypeCaller

gatk HaplotypeCaller -R /gatk/data/ref/ref.fasta -I data/bams/mother.bam \
-O /gatk/data/sandbox/variants.vcf

Note: Add JVM options to the command if you run into memory issues

gatk --java-options "-Xmx4G" HaplotypeCaller \
-R /gatk/data/ref/ref.fasta -I /gatk/data/bams/mother.bam \
-O /gatk/data/sandbox/variants.vcf

Run GVCF workflow tools using HaplotypeCaller, GenomicsDBImport and then GenotypeGVCFs to perform joint calling on multiple input samples.

Run HaplotypeCaller on three input bams (mother, father, son)

gatk HaplotypeCaller -R /gatk/data/ref/ref.fasta -I /gatk/data/bams/mother.bam -O /gatk/data/sandbox/mother.g.vcf -ERC GVCF

gatk HaplotypeCaller -R /gatk/data/ref/ref.fasta -I /gatk/data/bams/father.bam -O /gatk/data/sandbox/father.g.vcf -ERC GVCF

gatk HaplotypeCaller -R /gatk/data/ref/ref.fasta -I /gatk/data/bams/son.bam -O /gatk/data/sandbox/son.g.vcf -ERC GVCF

Run GenomicsDBImport on three GVCFs to consolidate

gatk GenomicsDBImport -V /gatk/data/sandbox/mother.g.vcf \
-V /gatk/data/sandbox/father.g.vcf \
-V /gatk/data/sandbox/son.g.vcf --genomicsdb-workspace-path \
/gatk/data/sandbox/trio.gdb_workspace --intervals 20

Alternatively, use CombinedGVCFs command as an alternative to GenomicsDBImport

gatk CombineGVCFs -R /gatk/data/ref/ref.fasta \
-V /gatk/data/sandbox/father.g.vcf \
-V /gatk/data/sandbox/mother.g.vcf -V /gatk/data/sandbox/son.g.vcf \
-O /gatk/data/sandbox/combine_trio_variants.vcf

Run GenotypeGVCFs on the GDB workspace to produce final multisample VCF

gatk GenotypeGVCFs -R /gatk/data/ref/ref.fasta \
-V gendb://data/sandbox/trio.gdb_workspace \
-G StandardAnnotation -O /gatk/data/sandbox/trio_variants.vcf

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