PCAdmix(out-of-date;upgrade to RFmix)

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# vcf2beagle
export JAVAHOME=/ifshk4/BC_PUB/biosoft/PIPE_RD/Package/java/jre1.8.0_45; /home/wanglizhong/software/vcftools/vcftools-build/bin/vcftools --gzvcf 00.vcf/1.vcf.gz --keep Ind.ChinaTau.list --recode -c | /home/wanglizhong/software/java/jre1.8.0_45/bin/java -jar /home/wanglizhong/software/beagle/Utilities/vcf2beagle.jar -9 01.vcf2beagle.pl.out/ChinaTau/1;gunzip 01.vcf2beagle.pl.out/ChinaTau/1.bgl.gz;
# PCAdmix
/home/wanglizhong/bin/PCAdmix3_linux -anc /ifshk4/BC_COM_P5/F13HTSNWKF0106/CATwiwR/project/11.PCAdmix/01.vcf2beagle.pl.out/LQC/1.bgl /ifshk4/BC_COM_P5/F13HTSNWKF0106/CATwiwR/project/11.PCAdmix/01.vcf2beagle.pl.out/indicus/1.bgl /ifshk4/BC_COM_P5/F13HTSNWKF0106/CATwiwR/project/11.PCAdmix/01.vcf2beagle.pl.out/taurus/1.bgl \
-adm /ifshk4/BC_COM_P5/F13HTSNWKF0106/CATwiwR/project/11.PCAdmix/01.vcf2beagle.pl.out/ChinaTau/1.bgl \
-map /ifshk4/BC_COM_P5/F13HTSNWKF0106/CATwiwR/project/11.PCAdmix/00.vcf/1.vcf.gz.map.map \
-rho /ifshk4/BC_COM_P5/F13HTSNWKF0106/CATwiwR/project/11.PCAdmix/00.vcf/1.vcf.gz.map.map.genetic_map.txt \
-lab LQC indicus taurus ChinaTau \
-w 100 -bed 1 -o chr1