Exome coordinates in Base Coverage Distribution with GATK
I want to run BaseCoverageDistribution in GATK with a .bam file over only exome intervals. Is there some kind of reference file with human exomes and exome coordinates I can use? The UCSC human exome coordinate reference file doesn't seem to be in a format that GATK will accept.
Thanks very much for your help,
Marcus G.
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marcusmgoldberg •
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marcusmgoldberg •
1 answer
Maybe you will be interested in this (Human Exome Capture Library Coordinates Download).
The interval format GATK accepted was introduced here (CommandLineGATK). It's easy to transform different interval formats.
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