Tagged with #findcoveredintervals
1 documentation article | 0 announcements | 2 forum discussions

No posts found with the requested search criteria.
Comments (1)


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 \ --activeRegionIn chr22.list 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

Comments (1)

Is there an existing tool to convert a GATK formatted interval list file (such as the one outputted by FindCoveredIntervals) to a BED file?