Mercurial > repos > dereeper > plink
diff Plink.pl @ 7:d6a7be1b5adb draft
Uploaded
author | dereeper |
---|---|
date | Wed, 07 Feb 2018 00:16:59 -0500 |
parents | fe39a4677281 |
children |
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--- 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");