# HG changeset patch
# User dereeper
# Date 1517980619 18000
# Node ID d6a7be1b5adb7558326ed3b0ec78f7c1c036d56d
# Parent da372a164001d8cfc37a81696bc1843a09778926
Uploaded
diff -r da372a164001 -r d6a7be1b5adb Plink.pl
--- 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");
diff -r da372a164001 -r d6a7be1b5adb find_indiv.py
diff -r da372a164001 -r d6a7be1b5adb plink.xml
--- a/plink.xml Wed Feb 07 00:15:42 2018 -0500
+++ b/plink.xml Wed Feb 07 00:16:59 2018 -0500
@@ -6,9 +6,11 @@
perl
+ perl-bioperl
plink
+