Mercurial > repos > wolma > mimodd
comparison vcf_filter.xml @ 0:6231ae8f87b8
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author | wolma |
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date | Wed, 11 Feb 2015 08:29:02 -0500 |
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children | a548b3c6ed00 |
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-1:000000000000 | 0:6231ae8f87b8 |
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1 <tool id="vcf_filter" name="VCF Filter"> | |
2 <description>Extracts lines from a vcf variant file based on field-specific filters</description> | |
3 <version_command>mimodd version -q</version_command> | |
4 <command> | |
5 mimodd vcf-filter | |
6 "$inputfile" | |
7 -o "$outputfile" | |
8 #if len($datasets): | |
9 -s | |
10 #for $i in $datasets | |
11 "$i.sample" | |
12 #end for | |
13 --gt | |
14 #for $i in $datasets | |
15 ## remove whitespace from free-text input | |
16 "#echo ("".join($i.GT.split()) or "ANY")#" | |
17 #echo " " | |
18 #end for | |
19 --dp | |
20 #for $i in $datasets | |
21 "$i.DP" | |
22 #end for | |
23 --gq | |
24 #for $i in $datasets | |
25 "$i.GQ" | |
26 #end for | |
27 #end if | |
28 #if len($regions): | |
29 -r | |
30 #for $i in $regions | |
31 #if $i.stop: | |
32 "$i.chrom:$i.start-$i.stop" | |
33 #else: | |
34 "$i.chrom:$i.start" | |
35 #end if | |
36 #end for | |
37 #end if | |
38 #if $vfilter: | |
39 --vfilter | |
40 ## remove ',' (and possibly adjacent whitespace) and replace with ' ' | |
41 "#echo ('" "'.join($vfilter.split(',')))#" | |
42 #end if | |
43 $vartype | |
44 </command> | |
45 | |
46 <inputs> | |
47 <param name="inputfile" type="data" format="vcf" label="VCF input file" /> | |
48 <repeat name="datasets" title="Sample-specific Filter" default="0" min="0"> | |
49 <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." /> | |
50 <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." /> | |
51 <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" /> | |
52 <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" /> | |
53 </repeat> | |
54 <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."> | |
55 <param name="chrom" type="text" label="Chromosome" /> | |
56 <param name="start" type="text" label="Region Start" /> | |
57 <param name="stop" type="text" label="Region End" /> | |
58 </repeat> | |
59 <param name="vartype" type="select" label="Select the types of variants to include in the output"> | |
60 <option value="">all types of variants</option> | |
61 <option value="--no-indels">exclude indels</option> | |
62 <option value="--indels-only">only indels</option> | |
63 </param> | |
64 <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." /> | |
65 </inputs> | |
66 | |
67 <outputs> | |
68 <data name="outputfile" format="vcf" /> | |
69 </outputs> | |
70 | |
71 <help> | |
72 .. class:: infomark | |
73 | |
74 **What it does** | |
75 | |
76 The tool filters a variant file in VCF format to generate a new VCF file with only a subset of the original variants. | |
77 | |
78 The following types of variant filters can be set up: | |
79 | |
80 1) Sample-specific filters: | |
81 | |
82 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. | |
83 | |
84 2) Region filters: | |
85 | |
86 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. | |
87 | |
88 3) Variant type filter: | |
89 | |
90 Filter variants by their type, i.e. whether they are single nucleotide variations (SNVs) or indels | |
91 | |
92 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. | |
93 The *sample* filter is included mainly 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. Besides, the filter can also be used to change the order of the samples since it will sort the samples in the order specified in the filter field. | |
94 | |
95 **Examples of sample-specific filters:** | |
96 | |
97 *Simple genotype pattern* | |
98 | |
99 genotype pattern: 1/1 ==> keep all variants in the vcf input file for which the specified sample's genotype is homozygous mutant | |
100 | |
101 *Complex genotype pattern* | |
102 | |
103 genotype pattern: 0/1, 0/0 ==> keep all variants for which the sample's genotype is either heterozygous or homozygous wildtype | |
104 | |
105 *Multiple sample-specific filters* | |
106 | |
107 Filter 1: genotype pattern: 0/0, Filter 2: genotype pattern 1/1: | |
108 ==> keep all variants for which the first sample's gentoype is homozygous wildtype **and** the second sample's genotype is homozygous mutant | |
109 | |
110 *Combining sample-specific filter criteria* | |
111 | |
112 genotype pattern: 1/1, depth of coverage: 3, genotype quality: 9 | |
113 ==> 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 | |
114 **and** at least three reads from the sample cover the variant site | |
115 | |
116 **TIP:** | |
117 | |
118 As in the example above, genotype quality is typically most useful in combination with a genotype pattern. | |
119 It acts then, effectively, to make the genotype filter more stringent. | |
120 | |
121 | |
122 | |
123 </help> | |
124 </tool> |