# phase
for i in {1..29}; do nohup java -Xmx60208m -jar /home/guoyingwei/software/beagle/beagle.18May20.d20.jar gt=leiqiong.filtered.snp.maf.vcf.gz out=chr${i}.leiqiong.filtered.snp.maf.phased chrom=$i & done
# conform-gt
for i in {1..26};do java -Xmx20g -jar /stor9000/apps/users/NWSUAF/2020055372/sheep_data/02.imputation/conform-gt.24May16.cee.jar gt=vcf ref=fef.vcf chrom=${i} match=POS out=out_${i};done
#impute
java -Xmx20g -jar /stor9000/apps/users/NWSUAF/2012010954/Software/beagle/beagle.28Sep18.793.jar gt=vcf ref=ref_vcf out=all_sample339.snp.filtered2.final.rename.imputation.ref