SEQanswers

SEQanswers (http://seqanswers.com/forums/index.php)
-   Bioinformatics (http://seqanswers.com/forums/forumdisplay.php?f=18)
-   -   GATK RealignerTargetCreator Error = Contigs do not match (http://seqanswers.com/forums/showthread.php?t=12310)

Hkins552 06-27-2011 07:20 AM

GATK RealignerTargetCreator Error = Contigs do not match
 
I'm trying to do a local realignment using GATK and seem to be stuck at the first step. I've created my ref.dict file and then tried the following script:

$ java -jar gatk -T RealignerTargetCreator -I input.bam -R genome.fasta -o output.intervals

An error was generated which said the contigs in my reference fasta and input bam do not match. Ex: Chrom 1 vs. 1

I attempted to use Picardtools ReorderSam command to at least order them correctly, but it will not recognize that "1" in the input.bam represents "chrom 1" in the reference. Is there a way to rename the contigs on one of these files such that ReorderSam can be used?

Thanks for your input!

Hkins552 07-01-2011 05:59 AM

Contigs Do Not Match
 
Still running into the same error. Any input would be greatly appreciated :) In the mean time, I will likely write a script to rename the contigs in the file and see if that pans out.


All times are GMT -8. The time now is 01:46 PM.

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