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comparison mutspecFilter.xml @ 7:eda59b985b1c draft default tip

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author iarc
date Mon, 13 Mar 2017 08:21:19 -0400
parents 46a10309dfe2
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6:46a10309dfe2 7:eda59b985b1c
10 mutspecFilter.pl 10 mutspecFilter.pl
11 --dir \$SCRIPT_PATH 11 --dir \$SCRIPT_PATH
12 $segDup 12 $segDup
13 $esp 13 $esp
14 $thG 14 $thG
15 #if str($FilterdbSNP.dbSNP) == "true" or $FilterdbSNP.dbSNP == True: 15 $exac
16 #if str($FilterdbSNP.dbSNP) == "true":
16 --dbSNP ${FilterdbSNP.column} 17 --dbSNP ${FilterdbSNP.column}
17 #else 18 #else
18 --dbSNP 0 19 --dbSNP 0
19 #end if 20 #end if
20 --refGenome ${refGenome} 21 --refGenome ${refGenome}
21 --outfile $output 22 --outfile $output
22 $input 23
24 #for $i, $filter in enumerate( $filters )
25 --filter $filter.reference
26 #end for
27
28 $input;
29
30
23 </command> 31 </command>
24 32
25 <inputs> 33 <inputs>
26 <param name="input" type="data" format="txt" label="Input file"/> 34 <param name="input" type="data" format="txt" label="Input file"/>
27 35
34 <when value="true"> 42 <when value="true">
35 <param name="column" type="data_column" data_ref="input" label="Select the dbSNP column for filtering" use_header_names="true" help="Select a column name snp or snpNonFlagged" /> 43 <param name="column" type="data_column" data_ref="input" label="Select the dbSNP column for filtering" use_header_names="true" help="Select a column name snp or snpNonFlagged" />
36 </when> 44 </when>
37 </conditional> 45 </conditional>
38 46
39 47 <param name="segDup" type="boolean" checked="true" truevalue="--segDup" falsevalue="" label="Filter against SegDup database" help="Remove variants present at &#62;= 0.9 frequency in the genomic duplicate segments database (Use only for human and mouse genomes)" />
40 <param name="segDup" type="boolean" checked="true" truevalue="--segDup" falsevalue="" label="Filter against SegDup database" help="Remove variants present at &#62;= 0.9 frequency in the genomic duplicate segments database" /> 48 <param name="esp" type="boolean" checked="true" truevalue="--esp" falsevalue="" label="Filter against the ESP database" help="Remove variants present at frequency &#62; 0.001 in the Exome Sequencing Project database (Use only for human genome)" />
41 <param name="esp" type="boolean" checked="true" truevalue="--esp" falsevalue="" label="Filter against the ESP database" help="Remove variants present at frequency &#62; 0.001 in the Exome Sequencing Project database (only valid for human genomes)" /> 49 <param name="thG" type="boolean" checked="true" truevalue="--thG" falsevalue="" label="Filter against the 1000g database project" help="Remove variants present at frequency &#62; 0.001 in the 1000 genome database (Use only for human genome)" />
42 <param name="thG" type="boolean" checked="true" truevalue="--thG" falsevalue="" label="Filter against the 1000g database project" help="Remove variants present at frequency &#62; 0.001 in the 1000 genome database (only valid for human genomes)" /> 50 <param name="exac" type="boolean" checked="true" truevalue="--exac" falsevalue="" label="Filter against the ExAC database" help="Remove variants present at frequency &#62; 0.001 in the EXome Agregate Consortium database (Use only for human genome)" />
51
52 <repeat name="filters" title="Additional filters">
53 <param name="reference" type="data" format="bed" label="Reference file (bed or vcf)" help="Remove variants present in the reference file"/>
54 </repeat>
55
43 </inputs> 56 </inputs>
44 57
45 <outputs> 58 <outputs>
46 <data type="data" name="output" format="tabular" label="${input.name.split(' ')[0]} filtered" /> 59 <data type="data" name="output" format="tabular" label="${input.name.split(' ')[0]} filtered" />
47 </outputs> 60 </outputs>
48 61
62 <stdio>
63 <regex match="Error message:" source="stderr" level="fatal" description="Read error message for more details" />
64 <regex match="Warning message:" source="stdout" level="warning" description="" />
65 </stdio>
66
49 <help> 67 <help>
50 68
51 **What it does** 69 **What it does**
52 70
53 Filter a file annotated with MutSpec-Annot tool. Variants present in public databases (dbSNP, SegDup, ESP, 1000 genome obtained from Annovar) will be removed from the input file (with frequency limits described above). 71 Filter a file annotated with MutSpec-Annot tool. Variants present in public databases obtained from Annovar will be removed from the input file (with frequency limits described above).
54 72
55 .. class:: warningmark 73 .. class:: warningmark
56 74
57 The databases ESP and 1000 genome can be used only for human genomes 75 The database genomic duplicate segments can be used only for human and mouse genomes
76
77 .. class:: warningmark
78
79 The databases ESP, 1000 genome and ExAC can be used only for human genome
58 80
59 -------------------------------------------------------------------------------------------------------------------------------------------------- 81 --------------------------------------------------------------------------------------------------------------------------------------------------
60 82
61 **Input** 83 **Input**
62 84
63 .. class:: warningmark 85 .. class:: warningmark
64 86
65 Tab delimited text files generated by MutSpec-Annot tool. 87 Tab delimited text files generated by MutSpec-Annot tool.
88
89 --------------------------------------------------------------------------------------------------------------------------------------------------
90
91 **Additional Filters**
92
93 .. class:: warningmark
94
95 You eventually would like to filter for additional features like repeats and tandem repeats.
96 You just need to provide the reference in vcf or bed format.
97
98 .. class:: infomark
99
100 Reference files are available on IARC Galaxy Shared Data.
101 On the top panel click on "Shared Data" and select "Data Libraries".
102 The category "BED annotations" contains reference files for different genomes.
103
66 104
67 -------------------------------------------------------------------------------------------------------------------------------------------------- 105 --------------------------------------------------------------------------------------------------------------------------------------------------
68 106
69 **Output** 107 **Output**
70 108
89 chr1 230846235 230846235 T A exonic AGT nonsynonymous SNV AGT:NM_000029:exon2:c.A362T:p.H121L NA NA NA NA - GTG chr1 230846235 230846235 T A 127 chr1 230846235 230846235 T A exonic AGT nonsynonymous SNV AGT:NM_000029:exon2:c.A362T:p.H121L NA NA NA NA - GTG chr1 230846235 230846235 T A
90 chr14 33290999 33290999 A G exonic AKAP6 nonsynonymous SNV AKAP6:NM_004274:exon13:c.A3980G:p.D1327G NA NA NA NA + GAC chr14 33290999 33290999 A G 128 chr14 33290999 33290999 A G exonic AKAP6 nonsynonymous SNV AKAP6:NM_004274:exon13:c.A3980G:p.D1327G NA NA NA NA + GAC chr14 33290999 33290999 A G
91 chr4 70156391 70156391 T C exonic UGT2B28 nonsynonymous SNV UGT2B28:NM_053039:exon5:c.T1172C:p.V391A score=0.949699;Name=chr4:70035680 NA 0.000199681 NA + GTA chr4 70156391 70156391 T C 129 chr4 70156391 70156391 T C exonic UGT2B28 nonsynonymous SNV UGT2B28:NM_053039:exon5:c.T1172C:p.V391A score=0.949699;Name=chr4:70035680 NA 0.000199681 NA + GTA chr4 70156391 70156391 T C
92 130
93 131
132 --------------------------------------------------------------------------------------------------------------------------------------------------
133
134 **Contact**
135
136 ardinm@fellows.iarc.fr; cahaisv@iarc.fr
137
138 --------------------------------------------------------------------------------------------------------------------------------------------------
139
140 **Code**
141
142 The source code is available on `GitHub`__
143
144 .. __: https://github.com/IARCbioinfo/mutspec.git
145
94 146
95 </help> 147 </help>
96 148
97 149
98 <citations> 150 <citations>