Entering edit mode
3.6 years ago
switch.reem
▴
40
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.
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' oror/and you can 'hard' filter the vcf by using the options '-e' or '-i' of
bcftools view