Statistical Analysis of VCF

Question

[Ishtiaq Ahmad Khan]

I have vcf file and want to calculate novel SNPs:

#CHROM      POS          ID              REF         ALT
chr1             3255           .                  C            T
chr1            14522           .                 G            A
chr1           15447   rs201635489         A             T
chr1           15585   rs533630043         G             C

I mean I want to calculate the number of SNPs with rs ID in column three

[russhh]

have you attempted anything yet?

[Ishtiaq Ahmad Khan]

I have annotated it using annovar and VEP, but I need a deep statistics such as correlation of SIFT, CADD, PolyPhen, Clinvar scores among different samples and so on. I have an statistical overview in VEP html output.

Answer 1

[Emily]

If you run it through the Ensembl VEP that's one of the statistics it will give you.