BED to RefSeq gene format

[gmarco]

Hello,

I would like to convert a BED interval file to RefSeq format. I need this to use it among with GATK DepthOfCoverage.

I've been trying loading custom track on UCSC. (http://genome.ucsc.edu/cgi-bin/hgTables) to get it converted without success.

Any tips?

[harryzs]

"GATK accept interval files for processing subsets of the genome in Picard-style interval lists"

http://www.broadinstitute.org/gatk/guide/article?id=1204

I think you just need to change your bed file to <Picard-style interval> format.

[gmarco]

Indeed it accepts -L option for specify intervals. But I want per gene coverage report. That's why I need to generate RefSeq file from BED.

[Ronic]

Hi gmarco, did u find the answer to your qeustion?? If yes please share it.