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