I am running into problem which has been asked in this forum but no right solution has be provided so far.
I have to regularly subset and merge several samples vcf during my data processing. But, I realize that a important information like
AF - allele frequency,
AC - allele count etc. aren't getting updated as need be.
I have used GATK and it is able to remove several sites that are: nonVariant, unused alternate, etc. etc. But, the important allele level information aren't getting update as required. I also tried VCF tools, BCFtools, vcf-merge but no help so far.
seems to be helpful, but there is problem with the installation because the of the required (old) package version.
Any suggestions ?