VAF liftover_field to pVCF

dnanexus-rnd / GLnexus

Scalable gVCF merging and joint variant calling for population sequencing projects

Apache License 2.0

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VAF liftover_field to pVCF #255

Open bopohdr opened 3 years ago

bopohdr commented 3 years ago

We need to have a VAF field present from DeepVariant in a pVCF generated by GLnexus. Is it possible to adjust .yaml file to also include the original VAF field into the pVCF ?

Thanks!

mlin commented 3 years ago

Is it an INFO field or a FORMAT field? The latter is relatively easy (but also VAF could be derived just-in-time from AD rather easily), the former not so much.

bopohdr commented 3 years ago

Hi,

it is a FORMAT field. I tried manipulating DeepVariant liftover, but unsuccessfully (I was not sure if its possible this way). We have thousands of samples, so we do not want to spend the resources by calculating VAF from AD, if VAF is already present in the gVCF.

Thanks!