|
0
|
1 <tool id="filter_vcf" name="Filter VCF" version="1.0">
|
|
|
2 <description>filters a VCF file</description>
|
|
|
3 <requirements>
|
|
|
4 <requirement type="package" version="2.7.10">python</requirement>
|
|
|
5 <requirement type="package" version="0.6.8dev">pyvcf</requirement>
|
|
|
6 <requirement type="package" version="3.11">pyyaml</requirement>
|
|
|
7 <requirement type="package" version="2.0.2">bintrees</requirement>
|
|
|
8 <requirement type="package" version="1.66">biopython</requirement>
|
|
|
9 <requirement type="package" version="1.4">matplotlib</requirement>
|
|
|
10 <requirement type="package" version="0.23.1">cython</requirement>
|
|
|
11 <requirement type="package" version="1.0">phephenix</requirement>
|
|
|
12 </requirements>
|
|
|
13 <stdio>
|
|
|
14 <!-- Assume anything other than zero is an error -->
|
|
|
15 <exit_code range="1:" />
|
|
|
16 <exit_code range=":-1" />
|
|
|
17 </stdio>
|
|
|
18 <command interpreter="bash">
|
|
|
19 filter_vcf.sh
|
|
|
20 $output
|
|
|
21 $input
|
|
6
|
22 $ref_fa
|
|
0
|
23 #if str($onlygood) == "false":
|
|
|
24 onlygood
|
|
|
25 #else
|
|
|
26 NOTTHERE
|
|
|
27 #end if
|
|
|
28 #for $sf in $snp_filter:
|
|
|
29 #for $name, $param in $sf.snp_filter_type.iteritems():
|
|
|
30 #if $name not in [ "__current_case__", "snp_filter_type_selector" ]:
|
|
|
31 ${name}:"${param}"
|
|
|
32 #end if
|
|
|
33 #end for
|
|
|
34 #end for
|
|
|
35 </command>
|
|
|
36
|
|
|
37 <inputs>
|
|
|
38 <param name="input" type="data" format="vcf" label="VCF File to filter" />
|
|
|
39
|
|
6
|
40 <param name="ref_fa" type="data" format="fasta" label="Reference genome fasta file" help="REQUIRED."/>
|
|
|
41
|
|
0
|
42 <repeat name="snp_filter" title="SNP Filter" help="">
|
|
|
43 <conditional name="snp_filter_type">
|
|
|
44 <param name="snp_filter_type_selector" type="select" label="SNP Filter Type">
|
|
|
45 <option value="gq_score_option">GQ score</option>
|
|
|
46 <option value="dp4_ratio_option">DP4 ratio</option>
|
|
|
47 <option value="ad_ratio_option">AD ratio</option>
|
|
|
48 <option value="mq_score_option">MQ score</option>
|
|
|
49 <option value="min_depth_option">Minimum depth</option>
|
|
|
50 <option value="uncall_gt_option">Uncall GT</option>
|
|
|
51 <option value="mq0_ratio_option">MQ0 ratio</option>
|
|
|
52 <option value="qual_score_option">Quality score</option>
|
|
|
53 <option value="mq0f_ratio_option">MQ0F ratio</option>
|
|
|
54 </param>
|
|
|
55 <when value="gq_score_option">
|
|
12
|
56 <param name="gq_score" type="integer" value="0" label="Minimum GC score" help="Type integer."/>
|
|
0
|
57 </when>
|
|
|
58 <when value="dp4_ratio_option">
|
|
12
|
59 <param name="dp4_ratio" type="float" value="0.9" label="Minimum DP4 ratio" help="Type float. Only samtools mpileup before version 1.3."/>
|
|
0
|
60 </when>
|
|
|
61 <when value="ad_ratio_option">
|
|
12
|
62 <param name="ad_ratio" type="float" value="0.9" label="Minimum AD ratio" help="Type float. GATK only and samtools from version 1.3."/>
|
|
0
|
63 </when>
|
|
|
64 <when value="mq_score_option">
|
|
12
|
65 <param name="mq_score" type="integer" value="30" label="Minimum MQ score" help="Type integer."/>
|
|
0
|
66 </when>
|
|
|
67 <when value="min_depth_option">
|
|
12
|
68 <param name="min_depth" type="integer" value="5" label="Minimum depth" help="Type integer."/>
|
|
0
|
69 </when>
|
|
|
70 <when value="uncall_gt_option">
|
|
|
71 <param name="uncall_gt" type="text" value="" hidden="True"/>
|
|
|
72 </when>
|
|
|
73 <when value="mq0_ratio_option">
|
|
12
|
74 <param name="mq0_ratio" type="float" value="0.05" label="Minimim MQ0 ratio" help="Type float. GATK only."/>
|
|
0
|
75 </when>
|
|
|
76 <when value="qual_score_option">
|
|
12
|
77 <param name="qual_score" type="integer" value="30" label="Minimim quality score" help="Type integer."/>
|
|
0
|
78 </when>
|
|
|
79 <when value="mq0f_ratio_option">
|
|
12
|
80 <param name="mq0f_ratio" type="float" value="0.05" label="Minimum MQ0F ratio" help="Type float. Samtools only."/>
|
|
0
|
81 </when>
|
|
|
82 </conditional>
|
|
|
83 </repeat>
|
|
|
84 <param name="onlygood" type="select" label="Write only good variants to output" help="Write only variants that PASS all filters. ">
|
|
|
85 <option value="true" selected="true">Write all</option>
|
|
|
86 <option value="false">Write only good</option>
|
|
|
87 </param>
|
|
|
88 </inputs>
|
|
|
89
|
|
|
90 <outputs>
|
|
|
91 <data format="vcf" name="output" label="${tool.name} on ${on_string}: filtered VCF" />
|
|
|
92 </outputs>
|
|
|
93 <tests>
|
|
|
94 <test>
|
|
|
95 <param name="input" value="test_input.vcf" ftype="vcf" />
|
|
|
96 <param name="min_depth" value="100" />
|
|
|
97 <output name="output" file="test_output.vcf" ftype="vcf" />
|
|
|
98 </test>
|
|
|
99 </tests>
|
|
|
100 <help>
|
|
|
101
|
|
|
102 usage: filter_vcf.py [-h] \-\-vcf VCF \-\-filters FILTERS \-\-output OUTPUT
|
|
|
103
|
|
|
104 optional arguments:
|
|
|
105
|
|
|
106 -h, \-\-help show this help message and exit
|
|
|
107
|
|
|
108 \-\-vcf VCF, -v VCF VCF file to (re)filter.
|
|
|
109
|
|
|
110 \-\-filters FILTERS, -f FILTERS Filter(s) to apply as key:threshold pairs, separated by comma.
|
|
|
111
|
|
|
112 \-\-output OUTPUT, -o OUTPUT Location for filtered VCF to be written.
|
|
|
113
|
|
6
|
114 \-\-reference REFERENCE, -r REFERENCE mpileup versions 1.3 and before do not output all positions. This is required to fix reference base in VCF.
|
|
|
115
|
|
|
116 \-\-only-good Write only variants that PASS all filters (default all variants are written).
|
|
|
117
|
|
15
|
118 -----
|
|
|
119
|
|
|
120 Which filter can be used for your data depends on the variant caller that was used to create the VCF file.
|
|
|
121
|
|
|
122 ============= ===============================================
|
|
|
123 Filter Remark
|
|
|
124 ============= ===============================================
|
|
|
125 GQ score Always available*
|
|
|
126 DP4 ratio Samtools mpileup before version 1.3 only*
|
|
|
127 AD ratio GATK and samtools mpileup from version 1.3 only
|
|
|
128 MQ score Always available*
|
|
|
129 Minimum depth Always available*
|
|
|
130 MQ0 ratio GATK only
|
|
|
131 Quality score Always available*
|
|
|
132 MQ0F ratio Samtools mpileup only*
|
|
|
133 ============= ===============================================
|
|
|
134
|
|
|
135 Filters marked with * are availabe for the workflow included with PHE Phenix.
|
|
|
136
|
|
0
|
137 </help>
|
|
|
138 </tool>
|
