Mercurial > repos > iuc > gemini_comp_hets

annotate gemini_comp_hets.xml @ 2:f52ad3dcee4e draft

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author iuc
date Tue, 16 Feb 2016 05:52:05 -0500
parents a511fb5bd380
children ac78943ce161
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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 <macros>
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4 <import>gemini_macros.xml</import>
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5 <token name="@BINARY@">comp_hets</token>
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6 </macros>
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7 <expand macro="requirements" />
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8 <expand macro="stdio" />
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9 <expand macro="version_command" />
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10 <command>
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11 <![CDATA[
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12 gemini @BINARY@
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14 #if $report.report_selector != 'all':
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15 --columns "${report.columns}"
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16 #end if
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18 @CMDLN_SQL_FILTER_FILTER_OPTION@
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19
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20 #if int($min_kindreds) > 0:
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21 --min-kindreds $min_kindreds
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22 #end if
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24 #if str($families).strip():
2
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25 --families "$families"
0
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26 #end if
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28 -d $d
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29 $allow_unaffected
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31 #if int($min_genotypequality) > 0:
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32 --min-gq $min_genotypequality
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33 #end if
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34
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35 #if int($gt_pl_max) != -1:
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36 --gt_pl_max $gt_pl_max
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37 #end if
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38
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39 $pattern_only
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40 --max-priority $max_priority
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41
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42
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43 "${ infile }"
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44 > "${ outfile }"
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45 ]]>
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46 </command>
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47 <inputs>
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48 <expand macro="infile" />
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49 <expand macro="column_filter" />
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50 <expand macro="filter" />
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51 <expand macro="min_kindreds" />
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52 <expand macro="family" />
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53 <expand macro="unaffected" />
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54 <expand macro="min_sequence_depth" />
2
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55 <param name="min_genotypequality" type="integer" value="0" min="0" label="The minimum genotype quality required for each sample in a family." help="default: 0 (--min-gq)" />
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56 <param name="gt_pl_max" type="integer" value="-1" min="-1" label="The maximum phred-scaled genotype (PL) allowed for each sample in a family." help="default: -1 not set (--gt-pl-max)" />
0
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57 <param name="pattern_only" type="boolean" truevalue="--pattern-only" falsevalue="" checked="False"
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58 label="Find compound hets by inheritance pattern, without regard to affection" help="(--pattern-only)"/>
2
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59 <param name="max_priority" type="integer" value="1" min="1" label="Default is to show only confident compound hets. Set to 2 or higher to include pairs that are less likely true comp-hets." help="default: 1 (--max-priority)" />
0
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60 </inputs>
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61 <outputs>
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62 <data name="outfile" format="tabular" />
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63 </outputs>
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64 <tests>
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65 <test>
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66 <param name="infile" value="gemini_comphets_input.db" ftype="gemini.sqlite" />
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67 <param name="report_selector" value="column_filter" />
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68 <param name="columns" value="chrom,start,end,ref,alt,gene,impact" />
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69 <param name="allow_unaffected" value="True" />
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70 <param name="max_priority" value="3" />
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71 <output name="outfile" file="gemini_comphets_result.tabular" />
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72 </test>
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73 </tests>
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74 <help>
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75 **What it does**
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76
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77 Many recessive disorders are caused by compound heterozygotes. Unlike canonical recessive sites where the same recessive allele is
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78 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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79 by two heterozygous recessive alleles at _different_ sites in a particular gene.
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80
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81 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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82 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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83 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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84 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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85
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86
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87 </help>
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88 <expand macro="citations"/>
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89 </tool>