Mercurial > repos > iuc > gemini
comparison gemini_comp_hets.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 |
|---|---|
| 1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0"> | |
| 2 <description>Identifying potential compound heterozygotes</description> | |
| 3 <expand macro="requirements" /> | |
| 4 <expand macro="version_command" /> | |
| 5 <macros> | |
| 6 <import>gemini_macros.xml</import> | |
| 7 <token name="@BINARY@">comp_hets</token> | |
| 8 </macros> | |
| 9 <command> | |
| 10 <![CDATA[ | |
| 11 gemini @BINARY@ | |
| 12 | |
| 13 #if $report.report_selector != 'all': | |
| 14 --columns "${report.columns}" | |
| 15 #end if | |
| 16 | |
| 17 #if $filter.filter_selector == 'yes': | |
| 18 --filter "${filter.filter}" | |
| 19 #end if | |
| 20 $only_affected | |
| 21 $ignore_phasing | |
| 22 | |
| 23 "${ infile }" | |
| 24 > "${ outfile }" | |
| 25 ]]> | |
| 26 </command> | |
| 27 <expand macro="stdio" /> | |
| 28 <inputs> | |
| 29 <param name="infile" type="data" format="sqlite" label="GEMINI database" /> | |
| 30 <expand macro="add_header_column" /> | |
| 31 <expand macro="column_filter" /> | |
| 32 <param name="only_affected" type="boolean" truevalue="--only-affected" falsevalue="" checked="False" | |
| 33 label="Report solely those compund heterozygotes impacted a sample labeled as affected" help="(--only-affected)"/> | |
| 34 <param name="ignore_phasing" type="boolean" truevalue="--ignore-phasing" falsevalue="" checked="False" | |
| 35 label="Ignore phasing when screening for compound hets" help="Candidates are inherently putative. (--ignore-phasing)"/> | |
| 36 <expand macro="filter" /> | |
| 37 </inputs> | |
| 38 <outputs> | |
| 39 <data name="outfile" format="tabular" label="${tool.name} on ${on_string}" /> | |
| 40 </outputs> | |
| 41 <tests> | |
| 42 <test> | |
| 43 </test> | |
| 44 </tests> | |
| 45 <help> | |
| 46 **What it does** | |
| 47 | |
| 48 Many recessive disorders are caused by compound heterozygotes. Unlike canonical recessive sites where the same recessive allele is | |
| 49 inherited from both parents at the _same_ site in the gene, compound heterozygotes occur when the individual’s phenotype is caused | |
| 50 by two heterozygous recessive alleles at _different_ sites in a particular gene. | |
| 51 | |
| 52 So basically, we are looking for two (typically loss-of-function (LoF)) heterozygous variants impacting the same gene at different loci. | |
| 53 The complicating factor is that this is _recessive_ and as such, we must also require that the consequential alleles at each heterozygous | |
| 54 site were inherited on different chromosomes (one from each parent). As such, in order to use this tool, we require that all variants are phased. | |
| 55 Once this has been done, the comp_hets tool will provide a report of candidate compound heterozygotes for each sample/gene. | |
| 56 | |
| 57 | |
| 58 @CITATION@ | |
| 59 </help> | |
| 60 <expand macro="citations"/> | |
| 61 </tool> |