Mercurial > repos > jjohnson > snpeff
annotate snpSift_filter.xml @ 4:fe23d90249ee
Remove help error copied wiki: and is single ampersand
author | Jim Johnson <jj@umn.edu> |
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date | Wed, 20 Mar 2013 13:19:14 -0500 |
parents | 2c595fea585c |
children | 192a236898f5 |
rev | line source |
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0 | 1 <tool id="snpSift_filter" name="SnpSift Filter" version="3.1"> |
2 <options sanitize="False" /> | |
3 <description>Filter variants using arbitrary expressions</description> | |
4 <!-- | |
5 You will need to change the path to wherever your installation is. | |
6 You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory) | |
7 java -Xmx6G -jar $JAVA_JAR_PATH/SnpSift.jar filter -f $input -e $exprFile > $output | |
8 --> | |
9 <requirements> | |
10 <requirement type="package" version="3.1">snpEff</requirement> | |
11 </requirements> | |
12 <command> | |
13 java -Xmx6G -jar \$JAVA_JAR_PATH/SnpSift.jar filter -f $input -e $exprFile > $output | |
14 </command> | |
15 <inputs> | |
16 <param format="vcf" name="input" type="data" label="VCF input"/> | |
17 <param name="expr" type="text" label="Expression" size="50"/> | |
18 </inputs> | |
19 <configfiles> | |
20 <configfile name="exprFile"> | |
21 $expr | |
22 </configfile> | |
23 </configfiles> | |
24 | |
25 <outputs> | |
26 <data format="vcf" name="output" /> | |
27 </outputs> | |
28 <stdio> | |
29 <exit_code range=":-1" level="fatal" description="Error: Cannot open file" /> | |
30 <exit_code range="1:" level="fatal" description="Error" /> | |
31 </stdio> | |
32 <help> | |
33 | |
1 | 34 **SnpSift filter** |
35 | |
36 You can filter ia vcf file using arbitrary expressions, for instance "(QUAL > 30) | (exists INDEL) | ( countHet() > 2 )". The actual expressions can be quite complex, so it allows for a lot of flexibility. | |
37 | |
38 Some examples: | |
39 | |
40 - *I want to filter out samples with quality less than 30*: | |
41 | |
42 * **( QUAL > 30 )** | |
43 | |
44 - *...but we also want InDels that have quality 20 or more*: | |
45 | |
46 * **(( exists INDEL ) & (QUAL >= 20)) | (QUAL >= 30 )** | |
0 | 47 |
1 | 48 - *...or any homozygous variant present in more than 3 samples*: |
49 | |
50 * **(countHom() > 3) | (( exists INDEL ) & (QUAL >= 20)) | (QUAL >= 30 )** | |
51 | |
52 - *...or any heterozygous sample with coverage 25 or more*: | |
53 | |
4
fe23d90249ee
Remove help error copied wiki: and is single ampersand
Jim Johnson <jj@umn.edu>
parents:
1
diff
changeset
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54 * **((countHet() > 0) & (DP >= 25)) | (countHom() > 3) | (( exists INDEL ) & (QUAL >= 20)) | (QUAL >= 30 )** |
1 | 55 |
56 - *I want to keep samples where the genotype for the first sample is homozygous variant and the genotype for the second sample is reference*: | |
57 | |
58 * **isHom( GEN[0] ) & isVariant( GEN[0] ) & isRef( GEN[1] )** | |
59 | |
60 | |
61 For complete details about this tool and epressions that can be used, please go to http://snpeff.sourceforge.net/SnpSift.html#filter | |
0 | 62 |
63 </help> | |
64 </tool> |