IndelRealigner with tumor-normal pair
Hi. I've run into a problem with the IndelRealigner when trying to use the -nWayOut argument. I have used a listofBAMs.list to provide one tumor-normal pair of BAMs (and this was used for the RealignerTargetCreator step with no problem). Otherwise my command looks something like this:
gatk/3.0-0/GenomeAnalysisTK.jar -T IndelRealigner -R genome.fa -I listofBAMs.list -nWayOut -targetIntervals file.intervals -known dbsnp_138.hg19.vcf -dt NONE
Can you see any problems?
This is the error output:
ERROR A USER ERROR has occurred (version 3.0-0-g6bad1c6):
ERROR MESSAGE: Invalid command line: Failed to parse value null for argument N_WAY_OUT. This is most commonly caused by providing an incorrect data type (e.g. a double when an int is required)
Thank you for your help.