GATK and hg19 reference.

[kasthuri]

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

[JohnK@Genome_Quest]

You could try to download liftOver program binary from the Kent Source Tree @ UCSC.

[ulz_peter]

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...

[kasthuri]

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.