I have a VCF file with multiple ambiguous ref/alt calls at some positions of the genome with ref allele type Y, R, M, K, S, W (i.e. two-base ambiguity codes). e.g.
3 60830534 . M C 101 . . GT:DP:A:C:G:T:PP:GQ 1/1:24:0,0:14,9:0,0:1,0:1038,0,808,782,114,898,883,114,101,806:101,
is there any way to remove them all from the VCF file?
Kind Regards sohail