I'm trying to switch to using the Phase 3 1000 genomes data from Phase I. In phase I, there was a indicator that said the variant type, so you could for example filter out SNPs easily with a grep command. However, they remove the below from Phase 3.
VT=SNP, indicates the variant is a snp.
VT=INDEL, indicates the variant is an indel,
VT=SV, indicates the variant is a deletion.
Anyone know if there's an easy way to filter out the SNPs? Is there another indicator in the file that I'm missing?