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5
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1 #!/bin/bash
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2
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3 tool_path=$(dirname $0)
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4
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5 filein=$1
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6 fileout_label=$2
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7 fileout=$3
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8 filelog=$4
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9 export=$5
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10 frequency=$6
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11 max_freq=$7
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12 allow_missing=$8
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13 nb_alleles_min=$9
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14 nb_alleles_max=${10}
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15 type=${11}
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16 bound_start=${12}
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17 bound_end=${13}
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18
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19
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20 if [ "${14}" != "None" ]
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21 then samples="--samples ${14}"
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22 fi
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23
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24 if [ "${15}" != "None" ]
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25 then chromosomes="--chromosomes ${15}"
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26 fi
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27
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28 if [ "$bound_start" -gt "$bound_end" ]
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29 then tmp=$bound_start ; bound_start=$bound_end ; bound_end=$tmp ; echo "Warning : Lower bound must be lower than greater bound!" >&2
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30 fi
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31
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32 if [ "$nb_alleles_min" -gt "$nb_alleles_max" ]
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33 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
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34 fi
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35
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36 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 $chromosomes
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37
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38 if [ "$export" = "VCF" ]
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39 then cp $fileout_label.recode.vcf $fileout ; rm $fileout_label.recode.vcf
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40 elif [ "$export" = "freq" ]
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41 then cp $fileout_label.frq $fileout ; rm $fileout_label.frq
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42 else cp $fileout_label.ped $fileout; cp $fileout_label.map ${16} ; rm $fileout_label.ped $fileout_label.map
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43 fi
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44
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45 cp vcftools.log $filelog
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46 rm vcftools.log
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