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Old 09-18-2011, 08:05 PM   #3
Location: Beijing

Join Date: Sep 2010
Posts: 11

Originally Posted by swbarnes2 View Post
Start by finiding a SNP that you see in IGV, and looking at the pileup in that position, and then the sam file in that region. Do the reads have good quality scores at the locus? Is the mapping quality alright? Something that I've observed, though it might not explain all your missing SNPs, is that sometimes, the BAQ calculations will mess up real SNPs, but not indels. I've occasionally seen this with sanger verified SNPs. So try rerunning mpileup with -B, see if that makes a difference.
Thanks for you reply.
I'm sure these SNPs should pass my fliter. The MAPQ, baseQ and depth is good enough. And no matter how low threshold be set, I did not got any SNPs anyway.
As -B option was already be used, I presumed you mean without it. That didn't help.

Perhaps I should give up and try other SNPcaller.

PS:GATK is really complicated. I'm trying.
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