Querying variations from a VCF file

Question

[Arko]

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!

[Pierre Lindenbaum]

d I'm trying to extract the type of variations (Substitution, Insertion, Silent, Intergenic, etc.)

see the questions about VEP/SnpeFF...

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.

see the VCF specification about FORMAT/AD.

Answer 1

[Emily]

This table is the ranking order Ensembl and the VEP use.