Filter gVCF files

[conmeehan]

Hi,

I am trying to apply the filtering process to gVCF field, where all the positions in the reference are in the VCF, However, when the filter is applied, it removes that line from the VCF instead of replacing with an N, as is needed in a VCF (i.e. now not all the positions are included in the output file). Is it possible to have a version of the tool where filtering is done by replacement with N instead of removing the SNP?

Thanks,
Conor