calculate ibd using beagle and germline

export JAVAHOME=/ifshk4/BC_PUB/biosoft/PIPE_RD/Package/java/jre1.8.0_45;
/ifshk4/BC_PUB/biosoft/PIPE_RD/Package/java/jre1.8.0_45/bin/java -jar /ifshk5/PC_HUMAN_EU/USER/wanglizhong/software/beagle/4.1/beagle.27Jul16.86a.jar ibd=true impute=false window=50000 overlap=20000 ibdlod=3 ibdtrim=1500 gt=$vcf out=$out/$chr

my $vcftools="/home/wanglizhong/software/vcftools/vcftools-build/bin/vcftools";
my $germline="/home/wanglizhong/software/germline/germline-1-5-1/germline";
my @vcf=<01.VCF/*vcf.gz>;
open(O,"> $0.sh");
foreach my $vcf(@vcf){
    print O "$vcftools --gzvcf $vcf --plink --out $vcf; ";
    print O "$germline -min_m 1 -bits 128 -err_hom 0 -err_het 4 < $vcf.run;n";
    open(O2,"> $vcf.run");
    print O2 "1n$vcf.mapn$vcf.pedn$vcf.outn";
    close O2;
}
close O;