Mercurial > repos > anton > vcffilter
annotate vcffilter.xml @ 1:fd10ad2f8f22
Updated to vcflib 86723982aa
author | Anton Nekrutenko <anton@bx.psu.edu> |
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date | Wed, 25 Jun 2014 16:14:19 -0400 |
parents | f84ad3b2d320 |
children | a1c14d64b003 |
rev | line source |
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0 | 1 <tool id="vcffilter" name="VCFfilter:" version="0.0.1"> |
2 <requirements> | |
1
fd10ad2f8f22
Updated to vcflib 86723982aa
Anton Nekrutenko <anton@bx.psu.edu>
parents:
0
diff
changeset
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3 <requirement type="package" version="86723982aa">vcflib</requirement> |
0 | 4 </requirements> |
5 <description>filter VCF data in a variety of attributes</description> | |
6 <command> | |
7 <!-- This tools depends on tabix functionality, which is currently distributed with Galaxy itself via a pysam egg --> | |
8 ln -s "${input1}" input1.vcf.gz && | |
9 ln -s "${Tabixized_input}" input1.vcf.gz.tbi && | |
10 vcffilter ${filterList} input1.vcf.gz > "${out_file1}" | |
11 </command> | |
12 | |
13 <inputs> | |
14 <param name="filterList" size="40" type="text" value="-f "DP > 10"" label="Specify filterting expression" help="See explanation of filtering options below"> | |
15 <sanitizer> | |
16 <valid initial="string.printable"> | |
17 <remove value="'"/> | |
18 </valid> | |
19 <mapping initial="none"> | |
20 <add source="'" target="__sq__"/> | |
21 </mapping> | |
22 </sanitizer> | |
23 </param> | |
24 <param format="vcf_bgzip" name="input1" type="data" label="From"> | |
25 <conversion name="Tabixized_input" type="tabix" /> | |
26 </param> | |
27 </inputs> | |
28 <outputs> | |
29 <data format="vcf" name="out_file1" /> | |
30 </outputs> | |
31 <tests> | |
32 <test> | |
33 <param name="filterList" value="-f "DP > 10""/> | |
34 <param name="input1" value="vcflib.vcf"/> | |
35 <output name="out_file1" file="vcffilter-test1.vcf"/> | |
36 </test> | |
37 </tests> | |
38 <help> | |
39 | |
40 You can specify the following option the **Specify filtering expression** box in any combination:: | |
41 | |
42 -f, --info-filter specifies a filter to apply to the info fields of records, removes alleles which do not pass the filter | |
43 -g, --genotype-filter specifies a filter to apply to the genotype fields of records | |
44 -s, --filter-sites filter entire records, not just alleles | |
45 -t, --tag-pass tag vcf records as positively filtered with this tag, print all records | |
46 -F, --tag-fail tag vcf records as negatively filtered with this tag, print all records | |
47 -A, --append-filter append the existing filter tag, don't just replace it | |
48 -a, --allele-tag apply -t on a per-allele basis. adds or sets the corresponding INFO field tag | |
49 -v, --invert inverts the filter, e.g. grep -v | |
50 -o, --or use logical OR instead of AND to combine filters | |
51 -r, --region specify a region on which to target the filtering (must be used in conjunction with -f or -g | |
52 | |
53 Filters are specified in the form {ID} {operator} {value}:: | |
54 | |
55 -f "DP > 10" # for info fields | |
56 -g "GT = 1|1" # for genotype fields | |
57 -f "CpG" # for 'flag' fields | |
58 | |
59 Any number of filters may be specified. They are combined via logical AND unless --or is specified on the command line. For convenience, you can specify "QUAL" to refer to the quality of the site, even though it does not appear in the INFO fields. | |
60 | |
61 Operators can be any of: =, !, <, >, pipe, & | |
62 | |
63 | |
64 To restrict output to a specific location use -r option (much be used in conjunction with -g or -f):: | |
65 | |
66 -r chr20:14000-15000 # only output calls between positions 14,000 and 15,000 on chromosome 20 | |
67 -r chrX # only output call on chromosome X | |
68 | |
69 ----- | |
70 | |
71 Vcffilter is a part of VCFlib toolkit developed by Erik Garrison (https://github.com/ekg/vcflib). | |
72 | |
73 </help> | |
74 </tool> |