[DOCKTESTERS] Help needed with DKFZ BiasFilter. Validation of DO52140. 100% match is wrong!

[Miguel Vazquez]

Dear all,

I just learnt that the DKFZ BiasFilter is NOT the OXOG filter workflow,
which means* I checked for the wrong thing in this validation!* I'm sorry
for the confusion.

Right now I pass the BAM files and the consensus.vcf (SNV_MNV) downloaded
from GNOS to the BiasFilter and compare the resulting VCF with the
consensus looking at the set of mutations containing the OXOGFAIL flag.
This apparently is not the comparison to make. *What is it that I need to
compare? is it the bPcr and bSeq flags?*

One first look at those flags do show quite some discrepancies
unfortunately on both donors (DO52140 and DO35937) for both flags. For
instance for DO35937 we find 11 mutations flaged bPcr with in the new
result, while the consensus.vcf only finds one, of them. Something similar
happens with the bSeq.

Can you please confirm this so I can come reply with a full report on this.

Kind regards, and sorry again for the confusion.

Miguel



On Mon, Feb 27, 2017 at 7:30 PM, Miguel Vazquez <miguel.vazquez at cnio.es>
wrote:

> Dear friends,
>
> I've performed the first test with the DKFZ BiasFilter and got a perfect
> match. There are 55 variants annotated with OXOGFAIL and they are the same
> in the input VCF file (consensus SNV/MNV VCF for that donor) and the output
> of the BiasFilter. I'm running the test on a second donor.
>
> Best regards
>
> Miguel
>
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