Mercurial > repos > wolma > mimodd
annotate vcf_filter.xml @ 12:c2c70edb70eb draft
Uploaded
| author | wolma |
|---|---|
| date | Mon, 25 Apr 2016 17:26:32 -0400 |
| parents | 93db2f9bca12 |
| children | c46406466625 |
| rev | line source |
|---|---|
|
9
93db2f9bca12
upgrade to v0.1.7.2
Wolfgang Maier wolfgang.maier@biologie.uni-freiburg.de
parents:
8
diff
changeset
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1 <tool id="vcf_filter" name="VCF Filter" version="0.1.7.2"> |
| 0 | 2 <description>Extracts lines from a vcf variant file based on field-specific filters</description> |
| 2 | 3 <macros> |
| 4 <import>toolshed_macros.xml</import> | |
| 5 </macros> | |
| 6 <expand macro="requirements"/> | |
| 0 | 7 <version_command>mimodd version -q</version_command> |
| 8 <command> | |
| 9 mimodd vcf-filter | |
| 10 "$inputfile" | |
| 11 -o "$outputfile" | |
| 12 #if len($datasets): | |
| 13 -s | |
| 14 #for $i in $datasets | |
| 15 "$i.sample" | |
| 16 #end for | |
| 17 --gt | |
| 18 #for $i in $datasets | |
| 19 ## remove whitespace from free-text input | |
| 20 "#echo ("".join($i.GT.split()) or "ANY")#" | |
| 21 #echo " " | |
| 22 #end for | |
| 23 --dp | |
| 24 #for $i in $datasets | |
| 25 "$i.DP" | |
| 26 #end for | |
| 27 --gq | |
| 28 #for $i in $datasets | |
| 29 "$i.GQ" | |
| 30 #end for | |
| 5 | 31 --af |
| 32 #for $i in $datasets | |
| 33 "#echo ($i.AF or "::")#" | |
| 34 #end for | |
| 0 | 35 #end if |
| 36 #if len($regions): | |
| 37 -r | |
| 38 #for $i in $regions | |
| 39 #if $i.stop: | |
| 40 "$i.chrom:$i.start-$i.stop" | |
| 41 #else: | |
| 42 "$i.chrom:$i.start" | |
| 43 #end if | |
| 44 #end for | |
| 45 #end if | |
| 46 #if $vfilter: | |
| 47 --vfilter | |
| 4 | 48 ## remove ',' and replace with ' ' |
| 0 | 49 "#echo ('" "'.join($vfilter.split(',')))#" |
| 50 #end if | |
| 51 $vartype | |
| 52 </command> | |
| 53 | |
| 54 <inputs> | |
| 55 <param name="inputfile" type="data" format="vcf" label="VCF input file" /> | |
| 56 <repeat name="datasets" title="Sample-specific Filter" default="0" min="0"> | |
| 57 <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." /> | |
| 58 <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." /> | |
| 59 <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" /> | |
| 60 <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" /> | |
| 5 | 61 <param name="AF" type="text" label="allelic fraction filter" help="expected format: [allele number]:[minimal fraction]:[maximal fraction]; keep only variants for which the fraction of sample-specific reads supporting a given allele number is between minimal and maximal fraction; if allele number is omitted, the filter operates on the most frequent non-reference allele instead" /> |
| 0 | 62 </repeat> |
| 63 <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."> | |
| 64 <param name="chrom" type="text" label="Chromosome" /> | |
| 65 <param name="start" type="text" label="Region Start" /> | |
| 66 <param name="stop" type="text" label="Region End" /> | |
| 67 </repeat> | |
| 68 <param name="vartype" type="select" label="Select the types of variants to include in the output"> | |
| 69 <option value="">all types of variants</option> | |
| 70 <option value="--no-indels">exclude indels</option> | |
| 71 <option value="--indels-only">only indels</option> | |
| 72 </param> | |
| 73 <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." /> | |
| 74 </inputs> | |
| 75 | |
| 76 <outputs> | |
| 77 <data name="outputfile" format="vcf" /> | |
| 78 </outputs> | |
| 79 | |
| 80 <help> | |
| 81 .. class:: infomark | |
| 82 | |
| 83 **What it does** | |
| 84 | |
| 85 The tool filters a variant file in VCF format to generate a new VCF file with only a subset of the original variants. | |
| 86 | |
| 87 The following types of variant filters can be set up: | |
| 88 | |
| 89 1) Sample-specific filters: | |
| 90 | |
| 91 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. | |
| 92 | |
| 93 2) Region filters: | |
| 94 | |
| 95 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. | |
| 96 | |
| 97 3) Variant type filter: | |
| 98 | |
| 99 Filter variants by their type, i.e. whether they are single nucleotide variations (SNVs) or indels | |
| 100 | |
| 101 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. | |
| 102 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. | |
| 103 | |
| 104 **Examples of sample-specific filters:** | |
| 105 | |
| 106 *Simple genotype pattern* | |
| 107 | |
| 108 genotype pattern: 1/1 ==> keep all variants in the vcf input file for which the specified sample's genotype is homozygous mutant | |
| 109 | |
| 110 *Complex genotype pattern* | |
| 111 | |
| 112 genotype pattern: 0/1, 0/0 ==> keep all variants for which the sample's genotype is either heterozygous or homozygous wildtype | |
| 113 | |
| 114 *Multiple sample-specific filters* | |
| 115 | |
| 116 Filter 1: genotype pattern: 0/0, Filter 2: genotype pattern 1/1: | |
| 117 ==> keep all variants for which the first sample's gentoype is homozygous wildtype **and** the second sample's genotype is homozygous mutant | |
| 118 | |
| 119 *Combining sample-specific filter criteria* | |
| 120 | |
| 121 genotype pattern: 1/1, depth of coverage: 3, genotype quality: 9 | |
| 122 ==> 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 | |
| 123 **and** at least three reads from the sample cover the variant site | |
| 124 | |
| 125 **TIP:** | |
| 126 | |
| 127 As in the example above, genotype quality is typically most useful in combination with a genotype pattern. | |
| 128 It acts then, effectively, to make the genotype filter more stringent. | |
| 129 | |
| 130 | |
| 131 | |
| 132 </help> | |
| 133 </tool> |