mocksu

Did you check the genomic coordinates of your datasets? They might be in different versions (e.g. hg37 vs hg38).

Never mind. I used rfmix 2.03 and it can take vcf files as input, which made the usage of rfmix much simpler.

My personal experience is that rfmix2 is the way to go. Alicia's tutorial is for rfmix1, and it's way too complicated to go through the data file preparation and format...

Hi Charles, We use linux for rfmix. I had spent months on rfmix1 without luck before switching to rfmix2. Maybe you could install linux OS on your mac? Best, Mousheng...

HI Vacanfield, Any update on this? I am fighting with a phasing error as well. I am trying to use rfmix2 to replicate Alicia Martin's HG02481, but the European segments...

> I am also wondering about this. I have a pretty simple scenario that I would expect RFmix to easily sort out, but there are numerous regions where average ancestry...

> Hi mocksu, > I've used some of the utilities in that pipeline, but I have not actually used the part that implements rfmix1. I briefly looked over the documentation...

Hi Patrick, This is good news! A few quick questions: * What do you mean by a reference phased VCF? Alicia's example uses shapeit reference based phasing. Did you do...

Hi Guilherme, As I said, we used eagle cohort phasing and it worked great. We did follow Alicia's online instructions to build the reference panel, though. A quite complicated process...