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comparison vcfToolsFilter.sh @ 0:9dec9f724a50 draft

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author dereeper
date Thu, 12 Feb 2015 15:37:31 -0500
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-1:000000000000 0:9dec9f724a50
1 #!/bin/bash
2
3 tool_path=$(dirname $0)
4
5 filein=$1
6 fileout_label=$2
7 fileout=$3
8 filelog=$4
9 export=$5
10 frequency=$6
11 max_freq=$7
12 allow_missing=$8
13 nb_alleles_min=$9
14 nb_alleles_max=${10}
15 type=${11}
16 bound_start=${12}
17 bound_end=${13}
18
19
20 if [ "${14}" != "None" ]
21 then samples="--samples ${14}"
22 fi
23
24 if [ "${15}" != "None" ]
25 then chromosomes="--chromosomes ${15}"
26 fi
27
28 if [ "$bound_start" -gt "$bound_end" ]
29 then tmp=$bound_start ; bound_start=$bound_end ; bound_end=$tmp ; echo "Warning : Lower bound must be lower than greater bound!" >&2
30 fi
31
32 if [ "$nb_alleles_min" -gt "$nb_alleles_max" ]
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
34 fi
35
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 $chromosomes
37
38 if [ "$export" = "VCF" ]
39 then cp $fileout_label.recode.vcf $fileout ; rm $fileout_label.recode.vcf
40 elif [ "$export" = "freq" ]
41 then cp $fileout_label.frq $fileout ; rm $fileout_label.frq
42 else cp $fileout_label.ped $fileout; cp $fileout_label.map ${16} ; rm $fileout_label.ped $fileout_label.map
43 fi
44
45 cp vcftools.log $filelog
46 rm vcftools.log