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(based on the Fst plot, let's use these boundaries: PAR: 0 - 2Mb, divergent: 4 - 17 Mb)
Where did the Y chromosome come from?
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#subset the vcf for the two regions vcftools --vcf chr12_for_phylo.vcf --chr chrXII --from-bp 0 --to-bp 2000000 --recode --out PAR vcftools --vcf chr12_for_phylo.vcf --chr chrXII --from-bp 4000000 --to-bp 17000000 --recode --out SDR #use vcf-kit to build trees vk phylo tree upgma PAR.recode.vcf > PAR.newick vk phylo tree upgma SDR.recode.vcf > SDR.newick #look at the trees on TACC with view_newick.py view_newick.py PAR.newick view_newick.py SDR.newick |
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