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1 <tool id="vcf_filter" name="VCF Filter">
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2 <description>extracts lines from a vcf variant file based on field-specific filters</description>
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3 <requirements>
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4 <requirement type="package" version="3.4.1">python3</requirement>
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5 <requirement type="package" version="0.1.3_9af04e0e9125">MiModD</requirement>
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6 </requirements>
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7 <command>
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8 mimodd vcf_filter
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9 $inputfile
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10 -o $outputfile
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11 #if len($datasets):
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12 -s
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13 #for $i in $datasets
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14 $i.sample
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15 #end for
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16 --gt
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17 #for $i in $datasets
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18 ## remove whitespace from free-text input
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19 #echo ("".join($i.GT.split()) or "ANY")
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20 #echo " "
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21 #end for
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22 --dp
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23 #for $i in $datasets
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24 $i.DP
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25 #end for
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26 --gq
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27 #for $i in $datasets
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28 $i.GQ
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29 #end for
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30 #end if
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31 #if len($regions):
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32 -r
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33 #for $i in $regions
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34 #if $i.stop:
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35 $i.chrom:$i.start-$i.stop
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36 #else:
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37 $i.chrom:$i.start
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38 #end if
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39 #end for
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40 #end if
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41 #if $vfilter:
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42 --v_filter
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43 ## remove ',' (and possibly adjacent whitespace) and replace with ' '
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44 #echo (" ".join("".join($vfilter.split()).split(',')))
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45 #end if
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46 $vartype
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47 </command>
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48
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49 <inputs>
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50 <param name="inputfile" type="data" format="vcf" label="VCF input file" />
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51 <repeat name="datasets" title="Sample-specific Filter" default="0" min="0">
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52 <param name="sample" type="text" label="sample" help="name of a sample as it appears in the VCF input file and that indicates the sample that this filter should be applied to." />
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53 <param name="GT" type="text" label="genotype pattern(s) for the inclusion of variants" help="keep only variants for which the genotype of the sample matches the specified pattern; format: x/x where x = 0 is wildtype and x = 1 is mutant. Multiple genotypes can be specified as a comma-separated list." />
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54 <param name="DP" type="integer" label="depth of coverage for the sample at the variant site" value = "0" help="keep only variants with at least this sample-specific coverage at the variant site" />
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55 <param name="GQ" type="integer" label="genotype quality for the variant in the sample" value = "0" help="keep only variants for which the genotype prediction for the sample has at least this quality" />
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56 </repeat>
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57 <repeat name="regions" title="Region Filter" default="0" min="0" help = "Filter variant sites by their position in the genome. If multiple Region Filters are specified, all variants that fall in ONE of the regions are reported.">
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58 <param name="chrom" type="text" label="Chromosome" />
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59 <param name="start" type="text" label="Region Start" />
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60 <param name="stop" type="text" label="Region End" />
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61 </repeat>
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62 <param name="vartype" type="select" label="Select the types of variants to include in the output">
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63 <option value="">all types of variants</option>
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64 <option value="--no_indels">exclude indels</option>
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65 <option value="--indels_only">only indels</option>
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66 </param>
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67 <param name="vfilter" type="text" label="sample" help="Filter output by sample name; only the sample-specific columns with their sample name matching any of the comma separated filters will be retained in the output." />
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68 </inputs>
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69
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70 <outputs>
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71 <data name="outputfile" format="vcf" />
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72 </outputs>
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73
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74 <help>
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75 .. class:: infomark
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76
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77 **What it does**
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78
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79 The tool filters a variant file in VCF format to generate a new VCF file with only a subset of the original variants.
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80
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81 The following types of variant filters can be set up:
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82
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83 1) Sample-specific filters:
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84
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85 Filter variants based on their characteristics in the sequenced reads of a specific sample. Multiple sample-specific filters are combined by logical AND, i.e., only variants that pass ALL sample-specific filters are kept.
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86
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87 2) Region filters:
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88
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89 Filter variants based on the genomic region they affect. Multiple region filters are combined by logical OR, i.e., variants passing ANY region filter are kept.
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90
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91 3) Variant type filter:
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92
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93 Filter variants by their type, i.e. whether they are single nucleotide variations (SNVs) or indels
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94
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95 In addition, the *sample* filter can be used to reduce the samples encoded in a multi-sample VCF file to just those specified by the filter.
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96 The *sample* filter is included for compatibility reasons: if an external tool cannot deal with the multisample file format, but instead looks only at the first sample-specific column of the file, you can use the filter to turn the multi-sample file into a single-sample file.
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97
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98 **Examples of sample-specific filters:**
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99
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100 *Simple genotype pattern*
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101
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102 genotype pattern: 1/1 ==> keep all variants in the vcf input file for which the specified sample's genotype is homozygous mutant
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103
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104 *Complex genotype pattern*
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105
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106 genotype pattern: 0/1, 0/0 ==> keep all variants for which the sample's genotype is either heterozygous or homozygous wildtype
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107
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108 *Multiple sample-specific filters*
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109
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110 Filter 1: genotype pattern: 0/0, Filter 2: genotype pattern 1/1:
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111 ==> keep all variants for which the first sample's gentoype is homozygous wildtype **and** the second sample's genotype is homozygous mutant
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112
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113 *Combining sample-specific filter criteria*
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114
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115 genotype pattern: 1/1, depth of coverage: 3, genotype quality: 9
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116 ==> keep variants for which the sample's genotype is homozygous mutant **and** for which this genotype assignment is corroborated by a genotype quality score of at least 9
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117 **and** at least three reads from the sample cover the variant site
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118
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119 **TIP:**
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120
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121 As in the example above, genotype quality is typically most useful in combination with a genotype pattern.
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122 It acts then, effectively, to make the genotype filter more stringent.
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123
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124
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125
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126 </help>
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127 </tool>
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