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Phylogenetics
| Code Block | |
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| title | Install VCF-kit | collapse | truecd phylogenetics |
Build gene trees from the PAR and from the divergent regions of chr12
(based on the Fst plot, let's use these boundaries: PAR: 0 - 2Mb, divergent: 4 - 17 Mb)
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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 |