Force calling at position

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Matt Wood

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Apr 28, 2017, 1:21:15 PM4/28/17

to Platypus Users

Is it possible to have Platypus call a variant at a position and output even if the ref is present?

I tried running with source and outputRefCalls, along with the args recommended for genotyping a list of known alleles:

--source=test.vcf.gz --minPosterior=0 --getVariantsFromBAMs=0 --outputRefCalls=1

But, I don't understand the results. I ended up with many more variant calls that I asked for in source, and the variant calls I wanted that do end up in the output file don't seem to be from the sample.

The test.vcf I'm using isn't a vcf generated from the sample. It's a vcf where I really only care about the chr and position. Is there another way to do this?

Thanks.

Andy Rimmer

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May 4, 2017, 3:43:08 AM5/4/17

to Matt Wood, Platypus Users

Hi Matt,

Can you send me a small example of the output? And the log file? With the options you set, Platypus should only be calling variants that are present in the input VCF file.

Kind regards,

Andy

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