I have a VCF file v4.1 and I'm trying to extract the type of variations (Substitution, Insertion, Silent, Intergenic, etc.) from it. If there are multiple possibilities, how would I annotate the most deleterious possibility? Apart from that, I'm trying to find the number of reads supporting the variant and the percentage of reads supporting the variant versus those supporting reference reads.
Can anyone elaborate on how to go about this? Thanks in advance!