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how to set the window size and step size for SNP files #111
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Hello,
XPEHH isn’t really computed in windows but snp by snp. If you only wanted
to compute these scores for a subset of the genome, I suppose you’d have to
subset your VCF before giving it to selscan. Is this what you were asking?
Zachary
Le ven. 10 mai 2024 à 07:36, hjt1129 ***@***.***> a écrit :
… hi,
we have SNP data, how to calculate xpehh value within specific window size
and step size. i found the "--pi", but it seem not work when set it with
following comand: selscan --xpehh --vcf vcf.file --vcf-ref vcf_ref.file
--map map.file --threads 8 --pi --pi-win 30000 --out out.file
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hi, |
Hello,
Ok so the —bp-wins parameter will convert the raw scores into z-scores and
then look for enrichments of extreme positive or extreme negative scores
within windows, this is typically how I identify regions putatively under
selection. You can read about this in Szpiech et al 2021 Evo Lett. This
paper is on XPNSL but it works the same for XPEHH.
Zachary
Le ven. 10 mai 2024 à 22:04, hjt1129 ***@***.***> a écrit :
… hi,
Thanks for your reply. No, i just want to calculate the whole genome VCF
in windows, like that calculate Fst using VCFTOOLS in windows and steps. So
it seems unachievable for XPEHH as you said. One more question, i see the
norm script which has the function to normlize xpehh values with windows by
"--bp-win" parameter, what's the underlying roles for normalizaton? and the
columums with "gt the fraction of XP-EHH scores >2" and "lt the fraction of
XP-EHH scores < -2" means the frequency of XP-EHH scores >2 and frequency
of XP-EHH scores < -2, respectively?
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hi,
we have SNP data, how to calculate xpehh value within specific window size and step size. i found the "--pi", but it seem not work when set it with following comand: selscan --xpehh --vcf vcf.file --vcf-ref vcf_ref.file --map map.file --threads 8 --pi --pi-win 30000 --out out.file
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