szpiech
commented
4 days ago Hello,
Selscan treats the allele coded as ‘1’ in the vcf as the derived allele and the allele coded as ‘0’ as the ancestral allele. If you have ancestral polarization information, you will need to process your vcf and flip allele codes accordingly.
It is all possible to run these analyses without polarizing your alleles, at a small power cost.
Zachary
Le mar. 19 nov. 2024 à 07:36, somnath-utu @.***> a écrit :
I’m using Selscan with VCF input files and have a question about how it determines the ancestral and derived states for alleles. Specifically: Does Selscan assume the REF allele in the VCF file is always the ancestral allele, and the ALT allele(s) are derived? How should the VCF file be formatted to ensure that Selscan correctly identifies ancestral and derived alleles for calculations like iHS or nSL?
Thank you for your clarification!
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I’m using Selscan with VCF input files and have a question about how it determines the ancestral and derived states for alleles. Specifically: Does Selscan assume the REF allele in the VCF file is always the ancestral allele, and the ALT allele(s) are derived? How should the VCF file be formatted to ensure that Selscan correctly identifies ancestral and derived alleles for calculations like iHS or nSL?
Thank you for your clarification!