Mercurial > repos > iuc > gemini
comparison gemini_lof_sieve.xml @ 0:720cbfb4190d draft
Imported from capsule None
| author | iuc |
|---|---|
| date | Mon, 25 Aug 2014 17:15:54 -0400 |
| parents | |
| children | 93bb0cfacefb |
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| -1:000000000000 | 0:720cbfb4190d |
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| 1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@version@.0"> | |
| 2 <description>Filter LoF variants by transcript position and type</description> | |
| 3 <expand macro="requirements" /> | |
| 4 <expand macro="version_command" /> | |
| 5 <macros> | |
| 6 <import>gemini_macros.xml</import> | |
| 7 <token name="@BINARY@">lof_sieve</token> | |
| 8 </macros> | |
| 9 <command> | |
| 10 <![CDATA[ | |
| 11 gemini @BINARY@ | |
| 12 "${ infile }" | |
| 13 > "${ outfile }" | |
| 14 ]]> | |
| 15 </command> | |
| 16 <expand macro="stdio" /> | |
| 17 <inputs> | |
| 18 <param name="infile" type="data" format="sqlite" label="GEMINI database" /> | |
| 19 </inputs> | |
| 20 <outputs> | |
| 21 <data name="outfile" format="tabular" label="${tool.name} on ${on_string}" /> | |
| 22 </outputs> | |
| 23 <tests> | |
| 24 <test> | |
| 25 </test> | |
| 26 </tests> | |
| 27 <help> | |
| 28 **What it does** | |
| 29 | |
| 30 Not all candidate LoF variants are created equal. For e.g, a nonsense (stop gain) variant impacting the first 5% of a polypeptide is far | |
| 31 more likely to be deleterious than one affecting the last 5%. Assuming you’ve annotated your VCF with snpEff v3.0+, the lof_sieve tool | |
| 32 reports the fractional position (e.g. 0.05 for the first 5%) of the mutation in the amino acid sequence. | |
| 33 In addition, it also reports the predicted function of the transcript so that one can segregate candidate | |
| 34 LoF variants that affect protein_coding transcripts from processed RNA, etc. | |
| 35 | |
| 36 @CITATION@ | |
| 37 </help> | |
| 38 <expand macro="citations"/> | |
| 39 </tool> |