Scott T Small

Hi All, Sorry for the lag. Here is a first draft proposal of a cross-coalescent function. I suppose my first thought is that it should take a tree rather than...

Hi @fenderglass, I am having the same issue as @bernard-kim details above. I followed hal#117 and grabbed the newest commit of hal2mafMP.py. The option errors are fixed but there is...

Hi @ksamuk, I implemented a version of Tajima's D that accounts for missing data. I tested it w/ the same scripts you used for the pixy publication, so hopefully a...

Hi @MilesLuca I havent made an effort to integrate code into the pixy base code. I am waiting to hear from @ksamuk whether this code addition met the standard and...

Hi Pontus, Sorry for being dense, but I dont see an attached version. Could you send me a link to the version please. I also noticed that --FAB option isnt...

I am also running into this issue. When I use -Smark and something like -Sp 0.5 there is the occasional case where the selected allele and a site in the...

Hi Brad, I am working on posting the file. Could you please comment on my question above: "If I was only going to use SNPs and not indels is it...

input vcf causing errors dropbox link: https://www.dropbox.com/s/2bhhh3bim2oyhtb/WbPNGL3-ALL.freebayesv0.9.20.out.vcf.gz?dl=0

thanks Brad, I will give this a try. One quick question, how do I use the {fix_ambig} pipe? I see it defined as "vcfutils" and imported into python, but couldnt...

To pick this back up. The majority of multiallelic sites are singletons. [Ref, Alt, Alt1, Alt2] percent singleton Alt1 : 0.5881852164112996 percent singleton Alt2 : 0.7144287770714822 percent singleton Alt1 &...