Mercurial > repos > gandres > vcftools_filter_stats_diversity
view vcftools_main/VCFToolFilter/vcfToolsFilter.sh @ 0:3b1436a9a6e5 draft
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author | gandres |
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date | Thu, 02 Jul 2015 05:21:40 -0400 |
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#!/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