Entering edit mode
6.4 years ago
hdtms
▴
20
Hi I tried to phase my Indel vcf file using BEAGLE and I got an error, I then read in these forum that BEAGLE can't be used for Indels. My question is: Is there another program to do this?
Phasing tools via omicsoft.
If I understood correctly OP already has identified the indels, but now wants to phase those. Beagle indeed only handles well behaving biallelic substitutions.