Entering edit mode
7.5 years ago
Curious3
•
0
It seems like the hap.py manual does not have a good example to explain the difference between using the -f option versus -T option. I used the -f option with a confident bed file but looks like the algorithm may not be using the bed file the way I thought it would. I would like all the variants in query vcf file that are compared with the truth vcf file to fall in the bed file regions provided. Could anyone help clarify?
Thanks!