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maxplanck-ie / snakepipes

Customizable workflows based on snakemake and python for the analysis of NGS data
http://snakepipes.readthedocs.io
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human reference genome, no_alt and PARY #1018

Open sunta3iouxos opened 1 month ago

sunta3iouxos commented 1 month ago

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 commented 1 month ago

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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

-- Reply to this email directly or view it on GitHub: https://github.com/maxplanck-ie/snakepipes/issues/1018 You are receiving this because you are subscribed to this thread.

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katsikora commented 1 month ago

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