human reference genome, no_alt and PARY

[sunta3iouxos]

Hi all,
I was wondering if the provided preindex sequences that are available for the snakepipes have taken into account the following:

from:
https://lh3.github.io/2017/11/13/which-human-reference-genome-to-use
https://www.biostars.org/p/342482/
Thank you

[NixBio]

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>> sunta3iouxos ***@***.***> 15.7.24 12:33 >>>

Hi all, I was wondering if the provided preindex sequences that are available for the snakepipes have taken into account the following: from: https://lh3.github.io/2017/11/13/which-human-reference-genome-to-use https://www.biostars.org/p/342482/ Thank you

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[katsikora]

Hi,

we have bundled ensembl genomes with snakePipes, I believe the "toplevel" fasta version.
Indeed, these might be affected by some of the issues mentioned by Heng Li in the blogpost you shared. We haven't optimized snakePipes for variant calling. I'm wondering if any of those issues would affect the allele-specific analyses though.

Best wishes,

Katarzyna