Mercurial > repos > jjohnson > snpeff

comparison snpSift_caseControl.xml @ 1:2c595fea585c

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Add more doocumentation
author Jim Johnson <jj@umn.edu>
date Wed, 30 Jan 2013 16:20:32 -0600
parents c07c403fc470
children a9bae7957c36
comparison
equal deleted inserted replaced
0:c07c403fc470 1:2c595fea585c
6 --> 6 -->
7 <requirements> 7 <requirements>
8 <requirement type="package" version="3.1">snpEff</requirement> 8 <requirement type="package" version="3.1">snpEff</requirement>
9 </requirements> 9 </requirements>
10 <command> 10 <command>
11 java -Xmx1G -jar \$JAVA_JAR_PATH/SnpSift.jar casControl -q $hhCase $hhControl $caseControStr $input > $output 11 java -Xmx1G -jar \$JAVA_JAR_PATH/SnpSift.jar casControl -q $hhCase $hhControl '$caseControStr' $input > $output
12 </command> 12 </command>
13 <inputs> 13 <inputs>
14 <param format="vcf" name="input" type="data" label="VCF input"/> 14 <param format="vcf" name="input" type="data" label="VCF input"/>
15 <param name="hhCase" type="select" label="Hom/Het case"> 15 <param name="hhCase" type="select" label="Hom/Het case">
16 <option value="any">Any</option> 16 <option value="any">Any</option>
20 <param name="hhControl" type="select" label="Hom/Het control"> 20 <param name="hhControl" type="select" label="Hom/Het control">
21 <option value="any">Any</option> 21 <option value="any">Any</option>
22 <option value="hom">Homozygous</option> 22 <option value="hom">Homozygous</option>
23 <option value="het">Heterozygous</option> 23 <option value="het">Heterozygous</option>
24 </param> 24 </param>
25 <param name="caseControStr" type="text" label="Case / Control" size="50"/> 25 <param name="caseControStr" type="text" label="Case / Control column designation" size="50">
26 <help>
27 Case and control are defined by a string containing plus and minus symbols {'+', '-', '0'} where '+' is case, '-' is control and '0' is neutral
28 </help>
29 <validator type="regex" message="must be only plus(+), minus(-), or zero(0) characters">[+-0]+</validator>
30 </param>
26 </inputs> 31 </inputs>
27 <outputs> 32 <outputs>
28 <data format="vcf" name="output" /> 33 <data format="vcf" name="output" />
29 </outputs> 34 </outputs>
30 <stdio> 35 <stdio>
32 <exit_code range="1:" level="fatal" description="Error" /> 37 <exit_code range="1:" level="fatal" description="Error" />
33 </stdio> 38 </stdio>
34 39
35 <help> 40 <help>
36 41
37 Count samples are in 'case' and 'control' groups. You can count 'homozygous', 'heterozygous' or 'any' variants. Case and control are defined by a string containing plus and minus symbols ('+' and '-') where '+' is case and '-' is control. This command adds two annotations to the VCF file. 42 **SnpSift CaseControl**
43
44 Allows you to count how many samples are in 'case' group and a 'control' group. You can count 'homozygous', 'heterozygous' or 'any' variants.
45
46 Case and control are defined by a string containing plus and minus symbols {'+', '-', '0'} where '+' is case, '-' is control and '0' is neutral.
47
48 This command adds two annotations to the VCF file:
49
50 - **CaseControl**: Two comma separated numbers numbers representing the number of samples that have the variant in the case and the control group. Example:
51
52 "CaseControl=3,4" *the variant is present in 3 cases and 4 controls.*
53
54
55 - **CaseControlP**: A p-value (Fisher exact test) that the number of cases is N or more. Example:
56
57 "CaseControl=4,0;CaseControlP=3.030303e-02" *in this case the pValue of having 4 or more cases and zero controls is 0.03*
58
59
60 For example, if we have ten samples (which means ten genotype columns in the VCF file), the first four are 'case' and the last six are 'control', so the description string would be "++++------". Let's say we want to distinguish genotypes that are homozygous in 'case' and either homozygous or heterozygous in 'control'. We would set:
61
62 - Hom/Het case = "hom"
63
64 - Hom/Het control = "any"
65
66 - Case / Control column designation = ""++++------"
67
38 68
39 For details about this tool, please go to http://snpeff.sourceforge.net/SnpSift.html#casecontrol 69 For details about this tool, please go to http://snpeff.sourceforge.net/SnpSift.html#casecontrol
40 70
41 </help> 71 </help>
42 </tool> 72 </tool>