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09-30-2013, 02:52 AM
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#1 |
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Member
Location: Spain Join Date: Oct 2012
Posts: 36
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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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09-30-2013, 05:18 AM
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#2 |
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Member
Location: Germany Join Date: Dec 2010
Posts: 29
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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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09-30-2013, 06:14 AM
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#3 |
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Member
Location: Spain Join Date: Oct 2012
Posts: 36
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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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01-26-2017, 06:17 AM
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#4 |
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Junior Member
Location: Mumbai Join Date: Jan 2017
Posts: 2
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Hi gmarco, did u find the answer to your qeustion?? If yes please share it.
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| Tags |
| bed, coverage, depthofcoverage, gatk, refseq |
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