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FindCoveredIntervals not recognizing --activeRegionIn option
I'm trying to run FindCoveredIntervals one chromosome at a time, so I'm using the --activeRegionIn option. However it doesn't seem to be reconized, no matter how I format it. For example, my basic command is like this:
java -Xmx3G -jar GenomeAnalysisTK.jar \
-T FindCoveredIntervals \
-R ucsc.hg19.fasta \
-I bwa.bam \
-o bwa.20xCov.chr22.list \
--minBaseQuality 17 \
--minMappingQuality 20 \
--coverage_threshold 20 \
I tried this two ways: 1) chr22.list file containing a single line "chr22" and 2) chr22.list file containing the line "chr22:1-51304566". In both cases, the interval walker starts with chr1:
INFO 13:15:48,925 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
INFO 13:15:48,925 ProgressMeter - | processed | time | per 1M | | total | remaining
INFO 13:15:48,926 ProgressMeter - Location | active regions | elapsed | active regions | completed | runtime | runtime
INFO 13:16:18,936 ProgressMeter - chr1:823974 16571.0 30.0 s 30.2 m 0.0% 31.1 h 31.1 h
I've tried "--activeRegionIn chr22" and "-AR chr22" as well, which both start processing at chr1.
Am I doing something wrong? Any ideas on how to get this to process data for an individual chromosome without splitting up the BAM file?
EDIT: I'm using GATK 3.2