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
have you attempted anything yet?
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.
If you run it through the Ensembl VEP that's one of the statistics it will give you.
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