Mercurial > repos > dereeper > snmf

changeset 1:395c7ab476a6 draft

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Uploaded
author dereeper
date Tue, 21 Jun 2016 19:38:29 -0400
parents 9a1729b89405
children 0c4267ccfbc1
files Snmf.pl
diffstat 1 files changed, 2 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- a/Snmf.pl	Tue May 17 10:51:34 2016 -0400
+++ b/Snmf.pl	Tue Jun 21 19:38:29 2016 -0400
@@ -35,9 +35,9 @@
 
 my $PLINK_EXE = "plink";
 
-system("$PLINK_EXE --vcf $input --allow-extra-chr --recode-vcf --out $directory/input >>$directory/plink.log 2>&1");
+system("$PLINK_EXE --vcf $input --allow-extra-chr --recode vcf-fid --out $directory/input >>$directory/logs 2>&1");
 
-system("vcf2geno $directory/input.vcf $directory/polymorphisms.geno >>$directory/vcf2geno.log 2>&1");
+system("vcf2geno $directory/input.vcf $directory/polymorphisms.geno >>$directory/logs 2>&1");
 
 
 my $ind_cmd = `grep '#CHROM' $input`;