HTSeqGenie (version 4.2.0)

gatk: gatk

Description

Run a command from the GATK

Usage

gatk(gatk.jar.path = getOption("gatk.path"), method, args, maxheap = "4g")

Arguments

gatk.jar.path

Path to the gatk jar file

method

Name of the gatk method, e.g. UnifiedGenotyper

args

additional args passed to gatk

maxheap

Maximal heap space allocated for java, GATK recommends 4G heap for most of its apps

Value

0 for success, stops otherwise

Details

Execute the GATK jar file using the method specified as arg. Stops if the command executed fails.