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-   -   BED to RefSeq gene format (http://seqanswers.com/forums/showthread.php?t=34131)

gmarco 09-30-2013 03:52 AM

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?

harryzs 09-30-2013 06:18 AM

"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.

gmarco 09-30-2013 07:14 AM

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 01-26-2017 07:17 AM

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


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