2017 Nov Taeyoung Lab note

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LD using Hapview

java -jar /alima9002/program/Haploview/Haploview.jar -nogui -out variant.SG.vcf.SNP.Q30.d5.hapview.out.rsq.%s -dprime -svg -compressedpng  -minMAF 0.01 -memory 1024 -haps %s -info %s.info -ldvalues NONE -ldcolorscheme RSQ -maxDistance 1000

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