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comparison snpSift_filter.xml @ 1:2c595fea585c

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Add more doocumentation
author Jim Johnson <jj@umn.edu>
date Wed, 30 Jan 2013 16:20:32 -0600
parents c07c403fc470
children fe23d90249ee
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0:c07c403fc470 1:2c595fea585c
29 <exit_code range=":-1" level="fatal" description="Error: Cannot open file" /> 29 <exit_code range=":-1" level="fatal" description="Error: Cannot open file" />
30 <exit_code range="1:" level="fatal" description="Error" /> 30 <exit_code range="1:" level="fatal" description="Error" />
31 </stdio> 31 </stdio>
32 <help> 32 <help>
33 33
34 You can filter using arbitrary expressions. 34 **SnpSift filter**
35 35
36 For details about this tool, please go to http://snpeff.sourceforge.net/SnpSift.html#filter 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 &gt; 30 )**
43
44 - *...but we also want InDels that have quality 20 or more*:
45
46 * **(( exists INDEL ) &amp; (QUAL >= 20)) | (QUAL >= 30 )**
47
48 - *...or any homozygous variant present in more than 3 samples*:
49
50 * **(countHom() > 3) | (( exists INDEL ) &amp; (QUAL >= 20)) | (QUAL >= 30 )**
51
52 - *...or any heterozygous sample with coverage 25 or more*:
53
54 * **((countHet() > 0) &amp;&amp; (DP >= 25)) | (countHom() > 3) | (( exists INDEL ) &amp; (QUAL >= 20)) | (QUAL >= 30 )**
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] ) &amp; isVariant( GEN[0] ) &amp; 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
37 62
38 </help> 63 </help>
39 </tool> 64 </tool>