How to convert Merlin phased result files to vcf

Question

[moxu]

I used Merlin to do family trio phasing. Merlin generated a .chr file and a .flow file for each chromosome. I need to convert these files to .vcf files, or at least to a format that is more modern and popular.

Any suggestions/recommendations would be highly appreciated.

Answer 1

[moxu]

The answer is that mega2 cannot take Merlin's .chr/.flow as input and cannot convert them to .vcf. The suggestion I got from the mega2 professor is to use shapeit, which can do trio phasing and can convert to vcf.