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Old 09-30-2013, 02:52 AM   #1
gmarco
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Question BED to RefSeq gene format

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?
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Old 09-30-2013, 05:18 AM   #2
harryzs
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"GATK accept interval files for processing subsets of the genome in Picard-style interval lists"
http://www.broadinstitute.org/gatk/g...rticle?id=1204

I think you just need to change your bed file to <Picard-style interval> format.
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Old 09-30-2013, 06:14 AM   #3
gmarco
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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.
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Old 01-26-2017, 06:17 AM   #4
Ronic
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Hi gmarco, did u find the answer to your qeustion?? If yes please share it.
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