Mercurial > repos > jjohnson > snpeff
annotate snpSift_caseControl.xml @ 7:b26a1aff7f81
Fix issues with snpEff commandline template and add test cases
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Thu, 28 Mar 2013 12:29:45 -0500 |
| parents | ec16dae84230 |
| children | 13b6ad2ddace |
| rev | line source |
|---|---|
| 0 | 1 <tool id="snpSift_caseControl" name="SnpSift CaseControl" version="3.1"> |
| 2 <description>Count samples are in 'case' and 'control' groups.</description> | |
| 3 <!-- | |
| 4 You will need to change the path to wherever your installation is. | |
| 5 You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory) | |
| 6 --> | |
| 7 <requirements> | |
| 8 <requirement type="package" version="3.1">snpEff</requirement> | |
| 9 </requirements> | |
| 10 <command> | |
|
2
a9bae7957c36
Fix typo on caseControl in commandline
Jim Johnson <jj@umn.edu>
parents:
1
diff
changeset
|
11 java -Xmx1G -jar \$JAVA_JAR_PATH/SnpSift.jar caseControl -q $hhCase $hhControl '$caseControStr' $input > $output |
| 0 | 12 </command> |
| 13 <inputs> | |
| 14 <param format="vcf" name="input" type="data" label="VCF input"/> | |
| 15 <param name="hhCase" type="select" label="Hom/Het case"> | |
| 16 <option value="any">Any</option> | |
| 17 <option value="hom">Homozygous</option> | |
| 18 <option value="het">Heterozygous</option> | |
| 19 </param> | |
| 20 <param name="hhControl" type="select" label="Hom/Het control"> | |
| 21 <option value="any">Any</option> | |
| 22 <option value="hom">Homozygous</option> | |
| 23 <option value="het">Heterozygous</option> | |
| 24 </param> | |
| 1 | 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> | |
| 0 | 31 </inputs> |
| 32 <outputs> | |
| 33 <data format="vcf" name="output" /> | |
| 34 </outputs> | |
| 35 <stdio> | |
| 36 <exit_code range=":-1" level="fatal" description="Error: Cannot open file" /> | |
| 37 <exit_code range="1:" level="fatal" description="Error" /> | |
| 38 </stdio> | |
| 5 | 39 <tests> |
| 40 | |
| 41 <test> | |
| 42 <param name="input" ftype="vcf" value="test.private.01.vcf"/> | |
| 43 <param name="hhCase" value="any"/> | |
| 44 <param name="hhControl" value="any"/> | |
| 45 <param name="caseControStr" value="--"/> | |
| 46 <output name="output"> | |
| 47 <assert_contents> | |
|
6
ec16dae84230
Fix tests for SnpSift caseControl and intervals
Jim Johnson <jj@umn.edu>
parents:
5
diff
changeset
|
48 <has_text text="CaseControl=0/0,0/2;" /> |
| 5 | 49 </assert_contents> |
| 50 </output> | |
| 51 </test> | |
| 52 | |
| 53 <test> | |
| 54 <param name="input" ftype="vcf" value="test.private.02.vcf"/> | |
| 55 <param name="hhCase" value="any"/> | |
| 56 <param name="hhControl" value="any"/> | |
| 57 <param name="caseControStr" value="--"/> | |
| 58 <output name="output"> | |
| 59 <assert_contents> | |
|
6
ec16dae84230
Fix tests for SnpSift caseControl and intervals
Jim Johnson <jj@umn.edu>
parents:
5
diff
changeset
|
60 <has_text text="CaseControl=0/0,2/0;" /> |
| 5 | 61 </assert_contents> |
| 62 </output> | |
| 63 </test> | |
| 64 | |
| 65 <test> | |
| 66 <param name="input" ftype="vcf" value="test.private.02.vcf"/> | |
| 67 <param name="hhCase" value="any"/> | |
| 68 <param name="hhControl" value="any"/> | |
| 69 <param name="caseControStr" value="-+"/> | |
| 70 <output name="output"> | |
| 71 <assert_contents> | |
|
6
ec16dae84230
Fix tests for SnpSift caseControl and intervals
Jim Johnson <jj@umn.edu>
parents:
5
diff
changeset
|
72 <has_text text="CaseControl=1/0,1/0;" /> |
| 5 | 73 </assert_contents> |
| 74 </output> | |
| 75 </test> | |
| 76 | |
| 77 </tests> | |
| 0 | 78 |
| 79 <help> | |
| 80 | |
| 1 | 81 **SnpSift CaseControl** |
| 82 | |
| 83 Allows you to count how many samples are in 'case' group and a 'control' group. You can count 'homozygous', 'heterozygous' or 'any' variants. | |
| 84 | |
| 85 Case and control are defined by a string containing plus and minus symbols {'+', '-', '0'} where '+' is case, '-' is control and '0' is neutral. | |
| 86 | |
| 87 This command adds two annotations to the VCF file: | |
| 88 | |
| 89 - **CaseControl**: Two comma separated numbers numbers representing the number of samples that have the variant in the case and the control group. Example: | |
| 90 | |
| 91 "CaseControl=3,4" *the variant is present in 3 cases and 4 controls.* | |
| 92 | |
| 93 | |
| 94 - **CaseControlP**: A p-value (Fisher exact test) that the number of cases is N or more. Example: | |
| 95 | |
| 96 "CaseControl=4,0;CaseControlP=3.030303e-02" *in this case the pValue of having 4 or more cases and zero controls is 0.03* | |
| 97 | |
| 98 | |
| 99 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: | |
| 100 | |
| 101 - Hom/Het case = "hom" | |
| 102 | |
| 103 - Hom/Het control = "any" | |
| 104 | |
| 105 - Case / Control column designation = ""++++------" | |
| 106 | |
| 0 | 107 |
| 108 For details about this tool, please go to http://snpeff.sourceforge.net/SnpSift.html#casecontrol | |
| 109 | |
| 110 </help> | |
| 111 </tool> |