SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
GATK: sorting vcf file given a reference file jorge Bioinformatics 4 01-14-2015 12:16 PM
hg19 genome reference for short read mapping yh253 Bioinformatics 4 12-29-2013 09:11 PM
How to get hg19.fa? ninad Bioinformatics 26 08-24-2011 07:40 AM
mitochondria reference HG19 or Cambridge foxyg Bioinformatics 1 09-16-2010 10:57 PM
construct whole genome reference for HG19 foxyg Bioinformatics 3 09-08-2010 01:12 PM

Reply
 
Thread Tools
Old 06-07-2011, 07:26 AM   #1
kasthuri
Member
 
Location: United States

Join Date: Jun 2011
Posts: 36
Default GATK and hg19 reference.

Hi,

We have mapped our SOLiD paired-end reads to UCSC's hg19. I am testing out GATK pipeline for calling SNP's. I am running into problems when doing the base recalibration step. GATK currently does not support hg19 aligned reads. The liftover GATK provided seems to run into java heap space errors. I can tweak the perl script they provided to increase the java space, but I am afraid this would run into too many work arounds. I don't want to map the reads again to hg18. Any thoughts on the ideal VCF to use for the hg19 aligned file?

Thanks
-Kasthuri
kasthuri is offline   Reply With Quote
Old 06-07-2011, 12:29 PM   #2
JohnK@Genome_Quest
Junior Member
 
Location: Worcester, MA

Join Date: Jun 2011
Posts: 7
Default

You could try to download liftOver program binary from the Kent Source Tree @ UCSC.
JohnK@Genome_Quest is offline   Reply With Quote
Old 06-07-2011, 08:55 PM   #3
ulz_peter
Senior Member
 
Location: Graz, Austria

Join Date: Feb 2010
Posts: 219
Default

Hi,
I wonder why that doesn't work as I recalibrate a lot of hg19 aligned reads with GATK... Which Reference file are you using.

Might have misunderstood your post, though...
ulz_peter is offline   Reply With Quote
Old 06-08-2011, 12:46 PM   #4
kasthuri
Member
 
Location: United States

Join Date: Jun 2011
Posts: 36
Default

I fixed the problem by tweaking the liftover perl script by the Broad. I use hg19 from UCSC. Part of the reason why it didn't work for me could be because I did not use bwa aligner or any aligner for that sake. The core facility here gives us the mapped files which were aligned by the native aligner supplied by the SOLiD. Thanks for your suggestions.

Last edited by kasthuri; 06-08-2011 at 12:49 PM.
kasthuri is offline   Reply With Quote
Reply

Tags
gatk, vcf

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 10:07 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO