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Principal Component Analysis
Use On personal computer, use the R script snp_pca.R to do PCA on the data. What's going on with chromosome 12?
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#(back on TACC)
#First choose a window size and step size (here 100Kb)
WINDOW_SIZE=100000
WINDOW_STEP=100000
#Run for chromosome 1
vcftools --vcf chrI.vcf \
--weir-fst-pop Pun_males.txt \
--weir-fst-pop Pun_females.txt \
--fst-window-size $WINDOW_SIZE \
--fst-window-step $WINDOW_STEP \
--out chrI_female_v_male
#chromosome 2
vcftools --vcf chrII.vcf \
--weir-fst-pop Pun_males.txt \
--weir-fst-pop Pun_females.txt \
--fst-window-size $WINDOW_SIZE \
--fst-window-step $WINDOW_STEP \
--out chrII_female_v_male
#chromosome12
vcftools --vcf chrXII.vcf \
--weir-fst-pop Pun_males.txt \
--weir-fst-pop Pun_females.txt \
--fst-window-size $WINDOW_SIZE \
--fst-window-step $WINDOW_STEP \
--out chrXII_female_v_male
#look at result files
ls -l *windowed.weir.fst
#send these to pungitius_exercise/ on personal computer to plot with R |
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#change to directory with species-separated vcfs
cd species_separated
#select window size and step (100Kb)
WINDOW_SIZE=100000
WINDOW_STEP=100000
#loop through vcfs and build commands for running --window-pi
>piCommands
for vcfFile in *.recode.vcf
do echo "vcftools --vcf $vcfFile --window-pi $WINDOW_SIZE --window-pi-step $WINDOW_STEP --out ${vcfFile/.recode.vcf} &" >> piCommands
done
#execute them
#look at results files
ls -l *windowed.pi
#send to pungitius_exercise/ on personal computer to plot with |
Plot the resulting *weir.fst and *.pi results with plot_window_stats.R
A pseudoautosomal region (PAR) is a region of a sex chromosome that still undergoes recombination.
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Phylogenetics
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(on TACC)
cd phylogenetics |
Build gene trees from the PAR and from the divergent regions of chr12
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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 |
For a nicer tree viewer, Dendroscope works well.
Build gene trees in windows along chromosome
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#set up boundaries
seq 0 250000 19750000 > lefts
seq 250000 250000 20000000 > rights
paste lefts rights > bounds.txt
#now build commands to subset the vcf with VCFtools, then pipe the subset into VCF-kit for tree building
awk '{print "vcftools --vcf chr12_for_phylo.vcf --chr chrXII --from-bp "$1 " --to-bp "$2" --recode -c | vk phylo tree upgma - > window_"$1"-"$2".newick &"}' bounds.txt > treeBuildCommands
#check the commands (should have 80 lines)
head treeBuildCommands
wc -l treeBuildCommands
#Double-check you are in an idev session
#If you are in an idev session, and had 80 lines, print to screen and execute
sh treeBuildCommands
#check that you have all trees
ls window*.newick | wc -l
#compile the resulting trees into a single file
#they need to be in order, so we can just simply cat them
#read bounds.txt again to cat them in order
echo ">allTrees.newick" >catTrees
while read bound
do left=$(echo $bound | cut -d " " -f 1)
right=$(echo $bound | cut -d " " -f 2)
echo "cat window_${left}-${right}.newick | tr -d '\n' >> allTrees.newick && echo '' >>allTrees.newick" >> catTrees
done<bounds.txt
#execute the catting commands
sh catTrees
#check that the input is correct size (should be 80)
wc -l allTrees.newick
#now run Twisst on them
~/twisst/twisst.py -t allTrees.newick\
-w topology_weights.tsvtxt\
-g Pun_X -g Pun_Y -g Sin -g Tym\
--groupsFile groups_file.txt\
--method threshold\
--thresholdTable ~/twisst/threshold_tables/binom_threshold_wilson_CI95_0.1.tsv
#This takes a bit.
#Once it's done, format the output
grep "^#" topology_weights.txt > topos.txt
grep -v "^#" topology_weights.txt > weights.txt
#send the results (all end in *.txt) to personal computer to plot with plot_twisst_results.R
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