Stephan Schiffels

For the record, a user contributed an MSMC2 package to conda: https://bioconda.github.io/recipes/msmc2/README.html?highlight=msmc2#package-package%20'msmc2'

Hi. Well, MSMC2 can fit a single global recombination rate, but not variable per genomic region. So I think what you describe wouldn't be possible.

As discussed via email, I think the issue is that your phased VCF is not recognised as being phased. Phased genotypes require a notation like `0|1` or `1|0`. If you...

Hi Shangzhe. I don’t understand. The two lines xReads += cov and xReads += cov if cov > 0 are exactly the same. If you add 0, it’s as if...

No, I think it should be xReads += cov. You want to calculate the mean coverage, and not-covered sites should not contribute. You want to compute "Total number of reads...

Well, two things: 1) The CCR midpoint was never meant as a principled "estimate for the split time" in a statistically rigorous sense. It is simply what it is: the...

Looks to me like pop2 and pop3 are hardly diverged at all. Have you checked with other statistics, like FST, or looked at whether the population sizes start to differ...

Goodness, sorry, and thanks for letting me know. I'll take a look ASAP.

I cannot reproduce this. When I run `conda install sequenctools` I get the right version with `This tool is part of sequenceTools version 1.6.0.0` at the bottom of the help...

This is a user error (I admit the error message isn't helpful): you choose eigenstrat output with `-e` which clashes with VCF output (`--vcf`). Remove the `-e`, then it will...