So I have a vcf file (myvar.vcf) and I want to do the following:-
1. Remove all mutations tagged as INDELS.
2. Consider mutaions that have a read depth greater than 100
3.To get all the mutations that occur in the tumor genome with respect to the control genome, we select all the mutations that have a genotype of 0/0 for the control genome and have a genotype of 1/1 or 0/1 for the tumor genome.
I have been trying all the three for quite a long time, but with no result. So can anyone help me with the steps? Thanks.