how can I mask vcf based on samples

Question

[switch.reem]

Hi all,

I am still experimenting with the bioinformatics field. so I would really appreciate your help.

I have a vcf file where I want to mask some entries in it based on samples. I am confused with all the literature , do I mask the vcf or do I mask the FAST file? do I put an N or and X? is there a tool that would help in masking certain parts of the VCF? I found GATK but what is that summary.tsv file, how do I get it?

I know I seem so lost, because I really am.

[Pierre Lindenbaum]

I have a vcf file where I want to mask some entries in it based on samples.

you can 'soft' filter the VCF by adding a new FILTER in the FILTER column for example using bcftools filter --soft-filter MY_FILTER_NAME (...) and the options '-e' or '-i' or

or/and you can 'hard' filter the vcf by using the options '-e' or '-i' of bcftools view