Yilei Fu
Yilei Fu
if you did not install methphaser via conda, these warnings can be caused by the wrong package version in you environment. If you installed conda it might be methphaser's issue,...
Hi Andreas, I would imagine this is an issue related to the read length or incomplete reference genome. I have only run MethPhaser before with the standard human genome reference...
Thanks, if this is the case there might be some chromosome name reading bug in MethPhaser, I will look into it and make it workable when the chromosome name is...
Should be a bug, could you please show me the vcf file? I have never used MethPhaser on mice samples so a little example could help.
I think that was because most human autosomes can be parsed as `int `but I can fix that, thanks for pointing out! Btw what is your reference genome headers like?...
I will download mm39 and take a look, thanks!
Yeah mm39 starts with something like `NC_000067.7` and HG38 starts with `chr22`. I will modify the dataframe reader, thanks for pointing that out
I think yes lowering -c and -a could be helpful, but this is a 100kb gap, is this in centromere region? might be too long for MethPhaser. However, happy to...
I just checked with my colleagues that are more familiar with HLA regions. We all found the coverage is not very nice in this region, and it would be better...
My intuitive hunch of this is that you can use child sample twice as one of the parent so that you can do trio phasing. Or you can try https://odelaneau.github.io/shapeit5/