Do Phasing with SHAPEIT

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export JAVA_HOME=/home/wanglizhong/software/java/jre1.8.0_45;
# beagle was used to improve genotype calls using genotype likelihoods
java -jar beagle/4.1/beagle.27Jul16.86a.jar gl=1.vcf.gz out=1.genotype;
# phase with shapeit
shapeit --thread 4 --effective-size 14269 --input-vcf 1.genotype.vcf.gz -M genetic_map_b37/genetic_map_chr1_combined_b37.txt --output-max 1.shapeit.haps 1.shapeit.sample --output-log 1.shapeit.log
# Convert the SHAPEIT haplotypes to vcf formats
shapeit -convert --input-haps 1.shapeit --output-vcf 1.shapeit.phased.vcf --output-log 1.shapeit.convert.log


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