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ComparativeGenomicsToolkit / cactus

Official home of genome aligner based upon notion of Cactus graphs
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ancestral reconstructed #1453

Open bighawkin opened 3 months ago

bighawkin commented 3 months ago

I would like to ask if the ancestral reconstructed sequences from the cactus software can be used for analyzing derived allele frequency. I have a VCF file for a population, how should I proceed?

glennhickey commented 3 months ago

I guess you'd create a MAF using the same reference genome as your VCF. The only other genome you'd need in the MAF is the ancestral genome (you can see its name using halStats --tree). This will give you an ancestral base for every (aligned) reference base, and you can use it to determine ancestral alleles in your VCF.

Look for a preprint by DongAhn Yoo et al. later this week where ancestors from a T2T ape alignment were used to derive ancestral alleles for human reference positions.

bighawkin commented 3 months ago

thank very much for your help！