Mercurial > repos > dereeper > plink
comparison Plink.pl @ 7:d6a7be1b5adb draft
Uploaded
author | dereeper |
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date | Wed, 07 Feb 2018 00:16:59 -0500 |
parents | fe39a4677281 |
children |
comparison
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6:da372a164001 | 7:d6a7be1b5adb |
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223 $bed_input =~s/\.bed//g; | 223 $bed_input =~s/\.bed//g; |
224 | 224 |
225 if (-e "$bed_input.bed"){ | 225 if (-e "$bed_input.bed"){ |
226 system("$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>$out.plink.stderr"); | 226 system("$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>$out.plink.stderr"); |
227 # for first 1000 SNPs | 227 # for first 1000 SNPs |
228 system("$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>$out.2.plink.stderr"); | 228 system("$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"); |
229 } | 229 } |
230 elsif (-e $bcf_input){ | 230 elsif (-e $bcf_input){ |
231 system("$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>$out.plink.stderr"); | 231 system("$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"); |
232 } | 232 } |
233 else | 233 else |