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probably at about 3 Mb |
Phylogenetics
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cd phylogenetics |
Build gene trees from Admixture
Run admixture on chromosome 1 and also the PAR and from the divergent regions region of chr12
(based on the Fst plot, let's use these boundaries: PAR: 0 - 2Mb, divergent: 4 - 17 Mb)
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#first switch to integers, because plink doesn't like roman numerals
sed 's/chrI/1/' chrI.vcf > chr1.vcf
sed 's/chrXII/12/' chrXII.vcf > chr12.vcf
#subset for the PAR and divergent region
vcftools --vcf chr12.vcf --chr 12 --from-bp 0 --to-bp 2000000 --recode --out PAR
vcftools --vcf chr12.vcf --chr 12 --from-bp 4000000 --to-bp 17000000 --recode --out SDR
#convert to bed files with plink
plink2 --vcf chr1.vcf --make-bed --out chr1 --allow-extra-chr
plink2 --vcf PAR.recode.vcf --make-bed --out PAR --allow-extra-chr
plink2 --vcf SDR.recode.vcf --make-bed --out SDR --allow-extra-chr
#run admixture
admixture chr1.bed 3
admixture PAR.bed 3
admixture SDR.bed 3
#send the *.Q files to personal computer to plot with plot_pungitius_admixture.R |
Phylogenetics
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cd phylogenetics |
Build gene trees from the PAR and from the divergent regions of chr12
Where did the Y chromosome come from?
...