SDIR=~/share; cd $SDIR/genotype_data; ls head -20 genotypes.ind head -20 genotypes.snp head -20 genotypes.geno | cut -c1-100 wc -l genotypes.ind wc -l genotypes.snp head -1 genotypes.geno | wc -c wc -l genotypes.geno awk '{print $3}' genotypes.ind | sort | uniq -c | head -20 awk '{print $3}' genotypes.ind | sort | uniq -c | awk '$1>1' | wc -l WDIR=~/work/share/solutions mkdir -p $WDIR cd $WDIR cat < pca.WestEurasia.params.txt genotypename: $SDIR/genotype_data/genotypes.geno snpname: $SDIR/genotype_data/genotypes.snp indivname: $SDIR/genotype_data/genotypes.ind evecoutname: $WDIR/pca.WestEurasia.evec evaloutname: $WDIR/pca.WestEurasia.eval poplistname: $SDIR/WestEurasia.poplist.txt lsqproject: YES numoutevec: 4 numthreads: 1 EOF cat pca.WestEurasia.params.txt time smartpca -p pca.WestEurasia.params.txt > pca.WestEurasia.log.txt WDIR=~/work/share/solutions mkdir -p $WDIR cd $WDIR cat < pca.AllEurasia.params.txt genotypename: $SDIR/genotype_data/genotypes.geno snpname: $SDIR/genotype_data/genotypes.snp indivname: $SDIR/genotype_data/genotypes.ind evecoutname: $WDIR/pca.AllEurasia.evec evaloutname: $WDIR/pca.AllEurasia.eval poplistname: $SDIR/AllEurasia.poplist.txt lsqproject: YES numoutevec: 4 numthreads: 1 EOF cat pca.AllEurasia.params.txt time smartpca -p pca.AllEurasia.params.txt WDIR=~/work/share/solutions mkdir -p $WDIR cd $WDIR cat < $WDIR/f3.poplist.txt Nganasan French Finnish Nganasan Icelandic Finnish Nganasan Lithuanian Finnish Nganasan Norwegian Finnish BolshoyOleniOstrov French Finnish BolshoyOleniOstrov Icelandic Finnish BolshoyOleniOstrov Lithuanian Finnish BolshoyOleniOstrov Norwegian Finnish EOF cat $WDIR/f3.poplist.txt WDIR=~/work/share/solutions mkdir -p $WDIR cd $WDIR cat < f3stats.params.txt genotypename: $SDIR/genotype_data/genotypes.smaller.geno snpname: $SDIR/genotype_data/genotypes.smaller.snp indivname: $SDIR/genotype_data/genotypes.smaller.ind popfilename: $WDIR/f3.poplist.txt inbreed: YES EOF cat f3stats.params.txt time qp3Pop -p f3stats.params.txt WDIR=~/work/share/solutions cat < $WDIR/dstat.poplist.txt Mbuti Nganasan French Finnish Mbuti Nganasan Icelandic Finnish Mbuti Nganasan Lithuanian Finnish Mbuti Nganasan Norwegian Finnish Mbuti BolshoyOleniOstrov French Finnish Mbuti BolshoyOleniOstrov Icelandic Finnish Mbuti BolshoyOleniOstrov Lithuanian Finnish Mbuti BolshoyOleniOstrov Norwegian Finnish EOF cat $WDIR/dstat.poplist.txt cat < $WDIR/dstats.params.txt genotypename: $SDIR/genotype_data/genotypes.geno snpname: $SDIR/genotype_data/genotypes.snp indivname: $SDIR/genotype_data/genotypes.ind popfilename: $WDIR/dstat.poplist.txt f4mode: YES EOF cat $WDIR/dstats.params.txt time qpDstat -p $WDIR/dstats.params.txt cat < $WDIR/outgroupf3stats.params.txt genotypename: $SDIR/genotype_data/genotypes.geno snpname: $SDIR/genotype_data/genotypes.snp indivname: $SDIR/genotype_data/genotypes.ind popfilename: $WDIR/outgroupF3pops_Han.txt EOF cat $WDIR/outgroupf3stats.params.txt time qp3Pop -p $WDIR/outgroupf3stats.params.txt cat < $WDIR/outgroupf3stats.params.txt genotypename: $SDIR/genotype_data/genotypes.geno snpname: $SDIR/genotype_data/genotypes.snp indivname: $SDIR/genotype_data/genotypes.ind popfilename: $WDIR/outgroupF3pops_MA1.txt EOF cat $WDIR/outgroupf3stats.params.txt time qp3Pop -p $WDIR/outgroupf3stats.params.txt