SEQanswers (
-   Bioinformatics (
-   -   BED to RefSeq gene format (

gmarco 09-30-2013 03:52 AM

BED to RefSeq gene format

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. ( 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"

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.

All times are GMT -8. The time now is 03:39 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.