Genotype Query Tools Fst Statistic

gistfile1.sh

wget --trust-server-names http://bit.ly/gqt_bcf
bcftools index chr11.11q14.3.bcf
gqt convert bcf -i chr11.11q14.3.bcf
wget --trust-server-names http://bit.ly/gqt_ped
head 1kg.phase3.ped
gqt convert ped -i chr11.11q14.3.bcf -p 1kg.phase3.ped
cat 1kg.phase3.ped | grep GBR | head
cat 1kg.phase3.ped | grep GBR | cut -f2 > GBR.txt
cat 1kg.phase3.ped | grep YRI | cut -f2 > YRI.txt
time vcftools \
    --bcf chr11.11q14.3.bcf \
    --weir-fst-pop GBR.txt \
    --weir-fst-pop YRI.txt \
    --out GBR_vs_YRI
time gqt fst \
    -i chr11.11q14.3.bcf.gqt \
    -d 1kg.phase3.ped.db \
    -p "Population = 'GBR'" \
    -p "Population = 'YRI'" \
   > GBR_vs_YRI.gqt.vcf
head GBR_vs_YRI.weir.fst
bcftools annotate \
    -x ^INFO/GQT_fst \
    GBR_vs_YRI.gqt.vcf \
    | grep -v "^##" \
    | cut -f1,2,8 \
    | sed -e "s/GQT_fst=//" \
    > GBR_vs_YRI.gqt.txt
paste GBR_vs_YRI.weir.fst GBR_vs_YRI.gqt.txt | grep -v nan | head