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1
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2 #!/usr/bin/perl
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3
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4 use strict;
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5 use Switch;
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6 use Getopt::Long;
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7 use Bio::SeqIO;
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8
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9 my $usage = qq~Usage:$0 <args> [<opts>]
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10
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11 where <args> are:
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12
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13 -i, --input <VCF input>
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14 -o, --out <Output basename>
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15
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16 <opts> are:
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17
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18 -s, --samples <Samples to be analyzed. Comma separated list>
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19 -c, --chromosomes <Chromosomes to be analyzed. Comma separated list>
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20 -e, --export <Output format (VCF/freq/plink. Default: VCF>
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21 -f, --frequency <Minimum MAF. Default: 0.001>
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22 -m, --max_freq <Maximum MAF. Default: 0.5>
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23 -a, --allow_missing <Allowed missing data proportion per site. Must be comprised between 0 and 1. Default: 1>
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24 -n, --nb_alleles <Accepted number of alleles (min,max). Default: 2,4>
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25 -t, --type <Type of polymorphisms to keep (ALL/SNP/INDEL). Default: ALL>
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26 -b, --bounds <Lower bound and upper bound for a range of sites to be processed (start,end). Default: 1, 100000000>
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27 ~;
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28 $usage .= "\n";
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29
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30 my ($input,$out);
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31
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32
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33 #my $indel_size_max = 500;
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34 #my $indel_size_min = 1;
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35 my $frequency_max = 0.5;
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36 my $frequency_min = 0.001;
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37 my $pos_max = 100000000000;
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38 my $pos_min = 0;
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39 my $filter_snp_type = "all";
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40
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41 my $missing_data = 1;
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42 my $export = "VCF";
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43 my $type = "ALL";
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44 my $nb_alleles;
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45 my $bounds;
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46 my $samples;
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47 my $chromosomes;
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48
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49 GetOptions(
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50 "input=s" => \$input,
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51 "out=s" => \$out,
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52 "samples=s" => \$samples,
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53 "chromosomes=s" => \$chromosomes,
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54 "frequency=s" => \$frequency_min,
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55 "max_freq=s" => \$frequency_max,
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56 "allow_missing=s"=> \$missing_data,
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57 "export=s" => \$export,
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58 "type=s" => \$type,
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59 "nb_alleles=s" => \$nb_alleles,
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60 "bounds=s" => \$bounds,
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61 );
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62
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63
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64 die $usage
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65 if ( !$input || !$out);
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66
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67
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68 my @dnasamples;
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69 if ($samples)
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70 {
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71 @dnasamples = split(",",$samples);
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72 }
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73 my @nalleles;
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74 if ($nb_alleles)
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75 {
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76 @nalleles = split(",",$nb_alleles);
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77 }
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78 my @boundaries;
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79 if ($bounds)
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80 {
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81 @boundaries = split(",",$bounds);
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82 }
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83 my @chromosomes_list;
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84 if ($chromosomes)
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85 {
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86 @chromosomes_list = split(",",$chromosomes);
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87 }
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88
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89
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90 my $experiment = "chromosomes";
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91 my $table = "";
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92 my %genes;
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93 my @snp_ids;
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94 my @snp_ids_and_positions;
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95 my @snp_ids_and_positions_all;
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96 my $gene;
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97 my $snp_num = 0;
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98 my %ref_sequences;
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99 my %snps_of_gene;
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100
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101
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102
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103
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104 my $indiv_cmd = "";
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105 if (@dnasamples)
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106 {
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107 $indiv_cmd = "--indv " . join(" --indv ",@dnasamples);
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108 }
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109
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110 my $chrom_cmd = "";
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111 if (@chromosomes_list)
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112 {
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113 $chrom_cmd = "--chr " . join(" --chr ",@chromosomes_list);
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114 }
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115
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116 my $export_cmd = "--recode";
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117 if ($export eq "freq")
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118 {
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119 $export_cmd = "--freq";
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120 }
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121 if ($export eq "plink")
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122 {
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123 $export_cmd = "--plink";
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124 }
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125
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126
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127
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128 my $nb_alleles_cmd = "--min-alleles 1 --max-alleles 4";
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129 if (@nalleles)
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130 {
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131 $nb_alleles_cmd = "--min-alleles $nalleles[0] --max-alleles $nalleles[1]";
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132 }
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133 my $bounds_cmd = "--from-bp 1 --to-bp 100000000";
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134 if (@boundaries)
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135 {
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136 $bounds_cmd = "--from-bp $boundaries[0] --to-bp $boundaries[1]";
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137 }
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138
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139
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140 my $type_cmd = "";
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141 if ($type eq "INDEL")
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142 {
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143 $type_cmd = "--keep-only-indels";
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144 }
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145 if ($type eq "SNP")
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146 {
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147 $type_cmd = "--remove-indels";
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148 }
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149
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150
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151 system("vcftools --vcf $input --out $out --keep-INFO-all --remove-filtered-all $type_cmd $export_cmd $chrom_cmd $indiv_cmd $nb_alleles_cmd --maf $frequency_min --max-maf $frequency_max --max-missing $missing_data >>vcftools.log 2>&1");
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152
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153
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154
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155
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156
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157
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158
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