diff VCFToolFilter/vcfToolsFilter.sh @ 2:ac7c9e40d601 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/VCFToolFilter/vcfToolsFilter.sh	Fri Jul 10 04:16:17 2015 -0400
@@ -0,0 +1,46 @@
+#!/bin/bash
+
+tool_path=$(dirname $0)
+
+filein=$1
+fileout_label=$2
+fileout=$3
+filelog=$4
+export=$5
+frequency=$6
+max_freq=$7
+allow_missing=$8
+nb_alleles_min=$9
+nb_alleles_max=${10}
+type=${11}
+bound_start=${12}
+bound_end=${13}
+
+
+if [ "${14}" != "None" ]
+then samples="--samples ${14}"
+fi
+
+if [ "${15}" != "None" ]
+then chromosomes="--chromosomes ${15}"
+fi
+
+if [ "$bound_start" -gt "$bound_end" ]
+then tmp=$bound_start ; bound_start=$bound_end ; bound_end=$tmp ; echo "Warning : Lower bound must be lower than greater bound!" >&2
+fi
+
+if [ "$nb_alleles_min" -gt "$nb_alleles_max" ]
+then tmp=$nb_alleles_min ; nb_alleles_min=$nb_alleles_max ; nb_alleles_max=$tmp ; echo "Warning : Minimum number of alleles must be lower than maximum number of allele!" >&2
+fi
+
+perl $tool_path/VCFToolsFilter.pl --input $filein --out $fileout_label --export $export --frequency $frequency --max_freq $max_freq --allow_missing $allow_missing --nb_alleles $nb_alleles_min','$nb_alleles_max --type $type --bounds $bound_start','$bound_end $samples $chromosomes
+
+if [ "$export" = "VCF" ]
+then cp  $fileout_label.recode.vcf $fileout ; rm $fileout_label.recode.vcf
+elif [ "$export" = "freq" ]
+then cp  $fileout_label.frq $fileout ; rm $fileout_label.frq
+else cp  $fileout_label.ped $fileout; cp $fileout_label.map ${16} ; rm $fileout_label.ped $fileout_label.map
+fi
+
+cp vcftools.log $filelog
+rm vcftools.log