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comparison Plink.pl @ 7:d6a7be1b5adb draft

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Uploaded
author dereeper
date Wed, 07 Feb 2018 00:16:59 -0500
parents fe39a4677281
children
comparison
equal deleted inserted replaced
6:da372a164001 7:d6a7be1b5adb
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