Command line option to the format of filtered genotype

[leandrogneves]

Hi Erik.

We were trying to add some filtering options to the genotype level in vcffilter. Mainly making it possible to replace the "." used for filtered genotype with a format of “./.:GQ:DP:RO:QR:AO:QA:GL” (e.g. ./.:11.8728:1:1:37:0:0:0,-0.30077,-3.22336) where the "./." at the beginning replaces the assigned genotype, but we keep the rest of the data. Preferably, the distinction between these two filtering choices would be decided from command line as a setting.

It would be helpful to know within the code:

-Where GT:GQ:DP:RO:QR:AO:QA:GL final values are stored before being filtered/best way to access them.
-Where the "." filtering is decided that replaces the data.
-Where command line options are evaluated.

Could you please point us in the right direction? We will share the new version with you in case you want to merge it to yours.

Thank you!
Leandro

[tseemann]

Suugest https://samtools.github.io/bcftools/bcftools.html#annotate