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# AlleleDepth (AD) values wrong after CombineVariants

I've seen related issues discussed here but not exactly this one. I'm following closely the current recommendations for an exome pipeline, and the GATK version,downloaded from git, was v2.5-2-gf57256b, Compiled 2013/06/06 17:28:57.

For example, I have two samples with heterozygous variants 12:81503433C>G. The AD values for the the samples in the raw vcf file, and the SNVs-only file were 15,14 and 20,15 for the two samples and these agree with what I see in IGV. There was nothing in the indels-only file at that position. The AD values were the same in the recalibrated SNVs-only file. But after combining the recalibrated SNVs and indels with CombineVariants the AD values inexplicably became 21,0 and 0,24 respectively. This seems to be happening to many variants.

Tagged:

Hi there,

Could you please upload some test files that reproduce the error so that we can debug this locally? Instructions are here: http://www.broadinstitute.org/gatk/guide/article?id=1894

Geraldine Van der Auwera, PhD

• ChinaMember Posts: 5

@Geraldine_VdAuwera said:
Hi there,

Could you please upload some test files that reproduce the error so that we can debug this locally? Instructions are here: http://www.broadinstitute.org/gatk/guide/article?id=1894

Hi,
I think I may get same problem with version v2.8-1-g932cd3a,
Is this problem had been solved?
thanks a lot!