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exome interval file for BaseCoverageDistribution

max_shpakmax_shpak Austin TXMember

I would like to obtain the coverage distribution on all exome intervals (human reference genome) using the BaseCoverageDistribution function in GATK. The problem I'm having is finding an appropriate reference file to associate with the -L argument. Specifically, the standard UCSC exome coordinate file doesn't have a format that GATK will accept, e.g. (header and first row given below, as opposed to chr1:start-stop) etc

name chrom strand cdsStart cdsEnd exonCount exonStarts exonEnds name2 exonFrames

NM_017582 chr1 - 154522913 154531029 13 154521050,154523413,154523872,154524246,154524396,1545
24568,154524879,154525211,154525507,154527210,154527903,154528335,154530702, 154522945,1545234
54528440,154531120, UBE2Q1 1,0,0,2,0,2,1,0,0,0,0,0,0,


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