UCSC refSeq to rod?

Kath · 01-13-2011, 02:45 AM

Hi,

I have downloaded the refSeq genes table from the UCSC website and wish to use it with the GATK IndelGenotyper tool. To do this apparently GATK requires reference-ordered data (rod). Does anyone know how to do this? Is there a script out there that I can use?

Thanks very much,

Kath

RockChalkJayhawk · 01-14-2011, 05:58 PM

Quote:

Originally Posted by Kath

Hi,

I have downloaded the refSeq genes table from the UCSC website and wish to use it with the GATK IndelGenotyper tool. To do this apparently GATK requires reference-ordered data (rod). Does anyone know how to do this? Is there a script out there that I can use?

Thanks very much,

Kath

Use this for information. Using the UCSC Table browser is another way.

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01-13-2011, 02:45 AM	#1
Kath Member Location: Oxford Join Date: Nov 2010 Posts: 24	UCSC refSeq to rod? Hi, I have downloaded the refSeq genes table from the UCSC website and wish to use it with the GATK IndelGenotyper tool. To do this apparently GATK requires reference-ordered data (rod). Does anyone know how to do this? Is there a script out there that I can use? Thanks very much, Kath