Hi,
I have been using the read-aware phasing method from shapeit2, but it stops the run due to some underflow error.
terminate called after throwing an instance of 'myException'
what(): Underflow in sequencing
So I would like to use the newest version (shapeit4), but there it is mandatory to use a genetic map file, which I don't have. So Is there a way of using only the read-based method with a .bam file as input? You recommend the Whatshap program as "pre-processing" for shapeit4? Or as an own method?
Hi, I have been using the read-aware phasing method from shapeit2, but it stops the run due to some underflow error.
So I would like to use the newest version (shapeit4), but there it is mandatory to use a genetic map file, which I don't have. So Is there a way of using only the read-based method with a .bam file as input? You recommend the Whatshap program as "pre-processing" for shapeit4? Or as an own method?