Mercurial > repos > dereeper > plink

diff Plink.pl @ 7:d6a7be1b5adb draft

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Uploaded
author dereeper
date Wed, 07 Feb 2018 00:16:59 -0500
parents fe39a4677281
children
line wrap: on
line diff
--- a/Plink.pl	Wed Feb 07 00:15:42 2018 -0500
+++ b/Plink.pl	Wed Feb 07 00:16:59 2018 -0500
@@ -225,7 +225,7 @@
 if (-e "$bed_input.bed"){
         system("$PLINK_EXE --bfile $bed_input --out $out $type_cmd $export_cmd $chrom_cmd $indiv_cmd $minfreq_cmd $maxfreq_cmd --geno $missing_data $thin_cmd $bounds_cmd --allow-extra-chr 1>$out.plink.stdout 2>$out.plink.stderr");
 	# for first 1000 SNPs
-	system("$PLINK_EXE --bfile $bed_input --out $out.recode $type_cmd --recode vcf-fid $chrom_cmd $indiv_cmd $minfreq_cmd $maxfreq_cmd --geno $missing_data $thin_cmd $bounds_cmd --allow-extra-chr --thin-count 800 1>$out.2.plink.stdout 2>$out.2.plink.stderr");
+	system("$PLINK_EXE $bed_input --out $out.recode $type_cmd --recode vcf-fid $chrom_cmd $indiv_cmd $minfreq_cmd $maxfreq_cmd --geno $missing_data $thin_cmd $bounds_cmd --allow-extra-chr --thin-count 800 1>$out.2.plink.stdout 2>$out.2.plink.stderr");
 }
 elsif (-e $bcf_input){
 	system("$PLINK_EXE --bcf $bcf_input --out $out $type_cmd $export_cmd $chrom_cmd $indiv_cmd $minfreq_cmd $maxfreq_cmd --geno $missing_data $thin_cmd $bounds_cmd --allow-extra-chr 1>$out.plink.stdout 2>$out.plink.stderr");