DongmeiDai

Thank you for your reply. Is the 2 of g=cNe2 the square of the effective population size? If the g=57667，Ne=30000， so the c is 0.000064, is it right? Thank you...

Hello, If I want to calculate β2 using an outgroup to call substitutions and ancestral alleles, can I just get epo files from outgroup vcf file, without common ancestor? Thank...

Thank you. I will try it ! If I use vcfm2acf to convert VCF to ACF , then I use usepopsrootanc to tell the root(outgroup), finally I use the replaceanc,...

Hello, I have another question. Is the file2.acf.gz in https://github.com/grenaud/glactools the result using the glactools with vcfm2acf --onlyGT --fai parameter? I am not sure if using these parameters is correct?...

Hello, the file1.acf.gz only have a outgroup individual:  when I use the "usepopsrootanc" parameter, I only tell the outgroup, then the error is as follows  I think it...

Hello, What does "ChimpHumanAncestor " refer to specifically? Thank you very much

Hello, Thank you for your reply! 1. May I ask if I have only root and ancestor, but no groups like other apes, is it OK to generate the follow...

I think I misunderstood your meaning. Is file4.acf.gz in your example (glactools replaceanc file2.acf.gz file3.acf.gz > file4.acf.gz) equal to the 1kg_chr6.AFRsubset.acf.gz in following code ( glactools vcfm2acf --onlyGT --epo all.epo.gz...

sorry， 1. glactools replaceanc file2.acf.gz file4.acf.gz 2. glactools vcfm2acf --onlyGT --epo all.epo.gz --fai human_g1k_v37.fasta.fai chr6.AFRsubset.recode.vcf > 1kg_chr6.AFRsubset.acf.gz What I understand is that if there is no epo file, file4 generated...

Yes, I used 3 commands to generate the file successfully. Since my species is not human, I want to know if the output file of 1 is the equivalent of...