# HG changeset patch
# User dereeper
# Date 1466552309 14400
# Node ID 395c7ab476a6c28b2242a649dfc1ba19faf62356
# Parent  9a1729b8940568310aeba25c860975bd678013d0
Uploaded

diff -r 9a1729b89405 -r 395c7ab476a6 Snmf.pl
--- 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`;