GATK

Genome Analysis Toolkit

How to use

gatk is available as a module on hadoop3.cesga.es

module load gatk

More info on how to use modules on the modules tutorial

Using SPARK tools

gatk uses hdfs when you launch a SPARK tool, check the hdfs tutorial for instructions.

gatk only supports SPARK on some tools, SPARK tools always end with Spark. Check the tool list here.

gatk ToolName toolArguments -- --spark-runner SPARK --spark-master yarn additionalSparkArguments

additionalSparkArguments can be used if a gatk job needs access to more resources, SPARK tutorial

Examples

gatk HaplotypeCallerSpark -L 1:1000000-2000000 -R hdfs://nameservice1/user/username/ref.fa -I hdfs://nameservice1/user/username/input.bam -O hdfs://nameservice1/user/username/output.vcf -- --spark-runner SPARK --spark-master yarn --driver-memory 4g --executor-memory 4g

gatk CalcMetadataSpark -I  hdfs://nameservice1/user/username/input.bam -O  hdfs://nameservice1/user/username/statistics.txt -- --spark-runner SPARK --spark-master yarn

Non SPARK tools

You can use standard gatk tools on hadoop3.cesga.es for testing but its not recommended