Entering edit mode
10.4 years ago
win
▴
970
I have a VCF file and I wanted to get only the count for insertion and deletions identified in the VCF. Is there any way to simply output the count of insertions and deletions from a VCF file?
Line representing indel has a "INDEL" tag in most of the vcf files. You now have to compare the reference sequence and alternate sequence to find out if the variant is an insertion or deletion.