Sebastian Schönherr comments

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                                            Sebastian Schönherr

Haplogrep error with a vcf-merge file.

Thanks, can you provide a minimal input file? Looks like there is a variant included in the file with an AF of ".". (We currently allow an AF of >...

Feature request: least common ancestor for equally scoring haplogroups

Hi Stephen, sorry for my late response. Makes sense to implement this directly in Haplogrep. I already talked to Pete at ASHG about this feature. For haplocheck we already implemented...

Issues with processing indels in VCF

Hi, Sorry for the late response. Can you provide an example so I can fix that.

Export FASTA using the command line version

Makes sense, we will add that!

haplogrep on non-human species

Hi Lel, Basically possible but you would to set up a tree structure similar to Phylotree.

Quality ∞% ?

Is this issue still open?

Haplogroup Quality score >1？

any chances that you can share the file? thanks!

Haplogroup Quality score >1？

Would be fantastic if you can give the latest version a try. For FASTA, we excluded heteroplasmis sites from the input profile (resulted in score > 1) and adapted the...

Haplogroup Quality score >1？

Thanks for the feedback, fyi the new version only fixes the FASTA related issues with the score. I'll look into the VCF problem, Hansi pointed out that this is related...

Navie question: Can I use this for Mouse mitochondrial varaint discovery?

only tested on human mtdna but from a computational perspective, yes.