Tagged with #findcoveredintervals
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Created 2012-07-23 23:55:42 | Updated 2012-07-23 23:55:42 | Tags: findcoveredintervals gatkdocs
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A new tool has been released!

Check out the documentation at FindCoveredIntervals.

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Created 2014-10-28 17:45:50 | Updated 2014-10-28 17:54:20 | Tags: findcoveredintervals active-regions
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Hi,

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?

Thanks,

Andrew

EDIT: I'm using GATK 3.2


Created 2013-07-15 14:01:25 | Updated | Tags: findcoveredintervals intervals
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Is there an existing tool to convert a GATK formatted interval list file (such as the one outputted by FindCoveredIntervals) to a BED file?