Exome coordinates in Base Coverage Distribution with GATK

Question

[marcusmgoldberg]

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.

Answer 1

[ghbore]

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.