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QualifyMissingIntervals - clarification on input files
Greetings GATK users,
I'm trying to run QualifyMissingIntervals in GATK, and want to verify the output of my command. I am using:
java -jar GenomeAnalysisTK.jar -T QualifyMissingIntervals -o outputtest.grp -R ref.fasta -I input.bam -L list.interval_list --targetsfile targets.intervals.
My interval list looks like this:
@HD VN:1.4 SO:coordinate @SQ SN:1 LN:4000000 chromosome 1 4000000 + target1
This is a subset of my targets file which was output from the RealignerTargetCreator function :
chromosome:889608-889611 chromosome:926218-926667 ... 24 lines
My output gives me data on only a single interval:
INTERVAL GC BQ MQ DP POS_IN_TARGET TARGET_SIZE BAITED MISSING_SIZE INTERPRETATION chromosome:1-4411709 0.65615955 31.01751693 42.77457476 421.83747409 -3522098 4 true 4000000 UNKNOWN
I get the feeling that one of my files is formatted improperly, but I can't figure out which it is. I have tried several iterations of the -L and --targetsfiles based on both the documentation and what has been previously posted on the forum, but to no avail, usually resulting in the command not running at all.
I would very much appreciate any help that might be provided!