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@kduyvesteyn
kduyvesteyn committed Feb 28, 2017
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2 changes: 1 addition & 1 deletion templates/Gender.sh.tt
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cd "[% dirs.tmp %]"

# same step as kinship, but easier to segregate and repeat (runs fast, saves a depedency)
# same step as kinship, but easier to segregate and repeat (runs fast, saves a dependency)
[% opt.VCFTOOLS_PATH %]/vcftools --temp "[% dirs.tmp %]" --out "[% dirs.tmp %]/gender_input" --vcf "[% vcf_path %]" --plink
cut -f 1-6 "[% dirs.tmp %]/gender_input.ped" > "[% dirs.tmp %]/gender_input.fam"

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