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Old 08-01-2013, 06:29 AM   #1
greggrant
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Location: philadelphia

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Default SNP calling using GATK and haplotypes

We're playing around here with SNP calling from illumina data. We generated 1.2 billion illumina reads of (one) human.

We've got about 70x coverage on average, but some regions sequenced with great imbalance between the two chromosomes causing GATK to make homogeneous calls where they should be hetero. This also seems to depend on the lane.

We were able to resolve the correct genotype at the questionable locations using haplotype information. So my question is, is there any way to make GATK use haplotype information like this, to fix the questionable calls or as a general quality control measure?

If not, is there some other package out there that does this? Possibly a post processor for GATK output?

Any information would be greatly appreciated! Thank you.

Last edited by greggrant; 08-01-2013 at 06:32 AM.
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