Mercurial > repos > iuc > gemini_inheritance
annotate gemini_inheritance.xml @ 3:2c68e29c3527 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit f7bdf08922aaf4119aefe7041e754a69cf64aebd
author | iuc |
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date | Wed, 13 Jul 2022 15:34:53 +0000 |
parents | 3123ce7acd0e |
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rev | line source |
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3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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1 <tool id="gemini_inheritance" name="GEMINI inheritance pattern" version="@VERSION@"> |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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2 <description>based identification of candidate genes</description> |
3
2c68e29c3527
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit f7bdf08922aaf4119aefe7041e754a69cf64aebd
iuc
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0
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3 <expand macro="bio_tools"/> |
0
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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4 <macros> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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5 <import>gemini_macros.xml</import> |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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6 <xml name="name_X"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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7 <param name="X" type="text" value="" |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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8 label="Alias to use for X chromosome" |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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9 help="The tool expects the X chromosome to be named 'X' or 'chrX'. If the reference genome used for variant calling had a different name for it, you will have to specify it here." /> |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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10 </xml> |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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11 </macros> |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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12 <expand macro="requirements" /> |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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13 <expand macro="stdio" /> |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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14 <expand macro="version_command" /> |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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15 <command> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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16 <![CDATA[ |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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17 gemini ${inheritance.pattern_type} |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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18 |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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19 #for $cond in $inheritance.constraint: |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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20 #set $filter = str($cond.filter).strip() |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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21 #if str($filter): |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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22 #if str($inheritance.pattern_type) == "comp_hets" and $cond.overwrite_default_filter: |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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23 --gene-where '$filter' |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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24 #else: |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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25 --filter '$filter' |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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26 #end if |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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27 #end if |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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28 #end for |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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29 |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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diff
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30 #if str($inheritance.pattern_type) in ("comp_hets", "mendel_errors"): |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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31 ${inheritance.by_pattern_only} |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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32 #end if |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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33 |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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34 ${inheritance.lenient} |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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35 ${inheritance.allow_unaffected} |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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36 |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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37 #if str($inheritance.pattern_type).startswith('x_linked_') and str($inheritance.X).strip(): |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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38 -X "${inheritance.X}" |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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39 #end if |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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40 |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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41 #if int($family_wise.min_kindreds) > 0: |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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42 --min-kindreds ${family_wise.min_kindreds} |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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43 #end if |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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44 |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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45 #if str($family_wise.families).strip(): |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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46 #set $families = ','.join([f.strip() for f in $family_wise.families.split(',')]) |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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47 --families "$families" |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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48 #end if |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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49 |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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50 #if int($family_wise.per_variant_selection.min_dp) > 0: |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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51 -d ${family_wise.per_variant_selection.min_dp} |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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52 #end if |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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53 |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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54 #if int($family_wise.per_variant_selection.min_gq) > 0: |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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55 --min-gq ${family_wise.per_variant_selection.min_gq} |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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56 #end if |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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57 |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
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58 #if int($family_wise.per_variant_selection.max_pl) > -1: |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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59 --gt-pl-max ${family_wise.per_variant_selection.max_pl} |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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60 #end if |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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61 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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62 #set $report = $oformat.report |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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63 @COLUMN_SELECT@ |
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64 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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65 "${ infile }" |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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66 > "${ outfile }" |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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67 ]]> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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68 </command> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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69 <inputs> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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70 <expand macro="infile" /> |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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71 <conditional name="inheritance"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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72 <param name="pattern_type" type="select" |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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73 label="Your assumption about the inheritance pattern of the phenotype of interest"> |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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74 <option value="autosomal_recessive">Autosomal recessive</option> |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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75 <option value="autosomal_dominant">Autosomal dominant</option> |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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76 <option value="x_linked_recessive">X-linked recessive</option> |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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77 <option value="x_linked_dominant">X-linked dominant</option> |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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78 <option value="de_novo">Autosomal de-novo</option> |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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79 <option value="x_linked_de_novo">X-linked de-novo</option> |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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80 <option value="comp_hets">Compound heterozygous</option> |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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81 <option value="mendel_errors">Violation of mendelian laws (LOH, plausible and implausible de-novo, uniparental disomy)</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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82 </param> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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83 <when value="comp_hets"> |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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84 <expand macro="insert_constraint"> |
3123ce7acd0e
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85 <expand macro="overwritable_where_default" default_where="exonic and high-impact variants (SQL clause: is_exonic = 1 or impact_severity != 'LOW')" /> |
3123ce7acd0e
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86 </expand> |
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87 <param argument="--pattern-only" name="by_pattern_only" type="boolean" truevalue="--pattern-only" falsevalue="" checked="false" |
3123ce7acd0e
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88 label="Ignore sample phenotypes during variant identification" |
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89 help="When turned on, the identification of compound heterozygous variant pairs gets based on the family tree only, i.e., the tool looks for heterozygous allele pairs in any kid that weren't occuring together in the parents (see the tool help below for the exact criteria used to detect compound heterozygosity)." /> |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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90 <expand macro="lenient" argument="--max-priority" truevalue="--max-priority 3" |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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91 help="When turned on, runs the tool with --max-priority 3 instead of the default value 1. This leads to inclusion of more ambiguous cases of compound heterozygosity." /> |
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92 <expand macro="unaffected" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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93 </when> |
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94 <when value="mendel_errors"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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95 <expand macro="insert_constraint" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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96 <param argument="--only-affected" name="by_pattern_only" type="boolean" truevalue="" falsevalue="--only-affected" checked="false" |
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97 label="Ignore sample phenotypes during variant identification" |
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98 help="When turned on, the identification of candidate variants gets based on the observed inheritance pattern only. The default is to report candidates only if there is evidence for them being phenotypically relevant, i.e., if they are observed in an affected sample." /> |
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99 <expand macro="lenient" /> |
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100 <param name="allow_unaffected" type="hidden" value="" /> |
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101 </when> |
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102 <when value="autosomal_recessive"> |
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103 <expand macro="insert_constraint" /> |
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104 <expand macro="lenient" /> |
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105 <expand macro="unaffected" /> |
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106 </when> |
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107 <when value="autosomal_dominant"> |
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108 <expand macro="insert_constraint" /> |
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109 <expand macro="lenient" /> |
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110 <expand macro="unaffected" /> |
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111 </when> |
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112 <when value="x_linked_recessive"> |
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113 <expand macro="insert_constraint" /> |
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114 <param name="lenient" type="hidden" value="" /> |
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115 <expand macro="unaffected" /> |
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116 <expand macro="name_X" /> |
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117 </when> |
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118 <when value="x_linked_dominant"> |
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119 <expand macro="insert_constraint" /> |
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120 <param name="lenient" type="hidden" value="" /> |
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121 <expand macro="unaffected" /> |
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122 <expand macro="name_X" /> |
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123 </when> |
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124 <when value="de_novo"> |
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125 <expand macro="insert_constraint" /> |
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126 <expand macro="lenient" /> |
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127 <expand macro="unaffected" /> |
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128 </when> |
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129 <when value="x_linked_de_novo"> |
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130 <expand macro="insert_constraint" /> |
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131 <param name="lenient" type="hidden" value="" /> |
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132 <expand macro="unaffected" /> |
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133 <expand macro="name_X" /> |
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134 </when> |
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135 </conditional> |
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136 <section name="family_wise" title="Family-wise criteria for variant selection" expanded="true"> |
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137 <expand macro="min_kindreds" /> |
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138 <param argument="--families" name="families" type="text" value="" |
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139 label="List of families to restrict the analysis to (comma-separated)" |
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140 help="Leave empty for an analysis including all families"/> |
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141 <conditional name="per_variant_selection"> |
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142 <param name="enabled" type="select" |
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143 label="Specify additional criteria to exclude families on a per-variant basis"> |
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144 <option value="no">No, analyze all variants from all included families</option> |
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145 <option value="yes">Yes, filter variants within families</option> |
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146 </param> |
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147 <when value="no"> |
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148 <param name="min_dp" type="hidden" value="0" /> |
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149 <param name="min_gq" type="hidden" value="0" /> |
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150 <param name="max_pl" type="hidden" value="-1" /> |
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151 </when> |
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152 <when value="yes"> |
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153 <param argument="-d" name="min_dp" type="integer" value="0" min="0" |
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154 label="Per-variant DP threshold for including a family" |
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155 help="All samples from a family must have a sequencing depth of at least this value at a given variant site in order for the family to be included in the analysis of this particular variant. default: 0 (do not apply this filter)" /> |
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156 <param argument="--min-gq" name="min_gq" type="integer" value="0" min="0" |
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157 label="per-variant GQ threshold for including a family" |
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158 help="The genotypes of all samples from a family must be called with at least this quality at a given variant site in order for the family to be included in the analysis of this particular variant. default: 0 (do not apply this filter)"> |
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159 </param> |
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160 <param argument="--gt-pl-max" name="max_pl" type="integer" value="-1" min="-1" |
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161 label="per-variant PL threshold for including a family" |
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162 help="The genotypes at a given variant site of all samples from a family must not have a higher (phred-scaled) likelihood to be wrong than this value in order for the family to be included in the analysis of this particular variant. default: -1 (do not apply this filter); if used the GEMINI documentation suggests 10 as a reasonable value" /> |
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163 </when> |
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164 </conditional> |
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165 </section> |
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166 <section name="oformat" title="Output - included information" expanded="true"> |
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167 <expand macro="column_filter" help="The tool reports key information about the inheritance pattern detection for each candidate variant found. It can precede each such row with additional columns, listing information about the variant taken from the variants table of the GEMINI database. Here, you can control which subset of the variants table columns should be added to the output."/> |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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168 </section> |
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169 </inputs> |
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170 <outputs> |
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171 <data name="outfile" format="tabular" |
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172 label="GEMINI ${inheritance.pattern_type} pattern on ${on_string}" /> |
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173 </outputs> |
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174 <tests> |
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175 <test> |
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176 <param name="infile" value="gemini_auto_dom_input.db" ftype="gemini.sqlite" /> |
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177 <conditional name="inheritance"> |
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178 <param name="pattern_type" value="autosomal_dominant" /> |
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179 <param name="lenient" value="true" /> |
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180 </conditional> |
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181 <conditional name="report"> |
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182 <param name="report_selector" value="minimal" /> |
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183 </conditional> |
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184 <output name="outfile"> |
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185 <assert_contents> |
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186 <has_line_matching expression="variant_id	gene	.*" /> |
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187 </assert_contents> |
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188 </output> |
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189 </test> |
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190 <test> |
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191 <param name="infile" value="gemini_auto_dom_input.db" ftype="gemini.sqlite" /> |
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192 <conditional name="inheritance"> |
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193 <param name="pattern_type" value="autosomal_dominant" /> |
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194 <param name="lenient" value="true" /> |
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195 </conditional> |
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196 <section name="oformat"> |
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197 <conditional name="report"> |
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198 <param name="report_selector" value="custom" /> |
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199 <param name="columns" value="gene,chrom,impact" /> |
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200 </conditional> |
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201 </section> |
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202 <output name="outfile"> |
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203 <assert_contents> |
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204 <has_line_matching expression="gene	chrom	impact.*" /> |
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205 </assert_contents> |
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206 </output> |
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207 </test> |
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208 <test> |
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209 <param name="infile" value="gemini_auto_dom_input.db" ftype="gemini.sqlite" /> |
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210 <conditional name="inheritance"> |
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211 <param name="pattern_type" value="autosomal_dominant" /> |
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212 <param name="lenient" value="true" /> |
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213 </conditional> |
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214 <section name="oformat"> |
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215 <conditional name="report"> |
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216 <param name="report_selector" value="custom" /> |
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217 <!-- test with empty multiselect list and columns specified |
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218 via text field instead --> |
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219 <param name="extra_cols" value="gene,chrom,impact" /> |
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220 </conditional> |
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221 </section> |
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222 <output name="outfile"> |
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223 <assert_contents> |
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224 <has_line_matching expression="gene	chrom	impact.*" /> |
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225 </assert_contents> |
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226 </output> |
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227 </test> |
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228 <test> |
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229 <param name="infile" value="gemini_auto_rec_input.db" ftype="gemini.sqlite" /> |
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230 <conditional name="inheritance"> |
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231 <param name="pattern_type" value="autosomal_recessive" /> |
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232 <param name="lenient" value="true" /> |
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233 </conditional> |
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234 <section name="oformat"> |
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235 <conditional name="report"> |
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236 <param name="report_selector" value="custom" /> |
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237 <param name="columns" value="gene,chrom,impact" /> |
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238 </conditional> |
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239 </section> |
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240 <output name="outfile"> |
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241 <assert_contents> |
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242 <has_line_matching expression="gene	chrom	impact.*" /> |
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243 </assert_contents> |
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244 </output> |
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245 </test> |
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246 <test> |
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247 <param name="infile" value="gemini_de_novo_input.db" ftype="gemini.sqlite" /> |
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248 <conditional name="inheritance"> |
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249 <param name="pattern_type" value="de_novo" /> |
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250 </conditional> |
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251 <section name="oformat"> |
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252 <conditional name="report"> |
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253 <param name="report_selector" value="custom" /> |
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254 <param name="columns" value="gene,ref,alt,impact" /> |
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255 </conditional> |
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256 </section> |
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257 <output name="outfile"> |
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258 <assert_contents> |
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259 <has_line_matching expression="gene	ref	alt	impact.*" /> |
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260 </assert_contents> |
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261 </output> |
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262 </test> |
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263 <test> |
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264 <param name="infile" value="gemini_comphets_input.db" ftype="gemini.sqlite" /> |
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265 <conditional name="inheritance"> |
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266 <param name="pattern_type" value="comp_hets" /> |
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267 <param name="lenient" value="true" /> |
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268 <param name="allow_unaffected" value="true" /> |
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269 </conditional> |
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270 <section name="oformat"> |
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271 <conditional name="report"> |
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272 <param name="report_selector" value="custom" /> |
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273 <param name="columns" value="chrom,start,end,ref,alt,gene,impact" /> |
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274 </conditional> |
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275 </section> |
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276 <output name="outfile"> |
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277 <assert_contents> |
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278 <has_line_matching expression="chrom	start	end	.*gene.*" /> |
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279 </assert_contents> |
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280 </output> |
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281 </test> |
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282 <test> |
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283 <param name="infile" value="gemini_de_novo_input.db" ftype="gemini.sqlite" /> |
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284 <conditional name="inheritance"> |
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285 <param name="pattern_type" value="mendel_errors" /> |
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286 </conditional> |
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287 <section name="oformat"> |
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288 <conditional name="report"> |
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289 <param name="report_selector" value="custom" /> |
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290 <param name="columns" value="gene,ref,alt,impact" /> |
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291 </conditional> |
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292 </section> |
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293 <output name="outfile"> |
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294 <assert_contents> |
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295 <has_line_matching expression="gene	ref	alt	impact	.*violation.*" /> |
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296 </assert_contents> |
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297 </output> |
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298 </test> |
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299 </tests> |
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300 <help> |
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301 <![CDATA[ |
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302 |
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303 **What it does** |
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304 |
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305 Assuming you have defined the familial relationships between samples when |
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306 loading your VCF into GEMINI, you can use this tool to identify candidate genes |
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307 and variants that explain the inheritance pattern of a phenotype of interest. |
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308 |
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309 **Inheritance pattern detection rules** |
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310 |
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311 *Autosomal recessive* |
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312 |
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313 Criteria: |
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314 |
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315 - all affected must be hom_alt |
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316 - [affected] no unaffected can be hom_alt (can be unknown) |
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317 - [default] if parents exist they must be unaffected and het for all affected kids |
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318 - [default] if there are no affecteds that have a parent, a warning is issued. |
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319 |
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320 If ``--lenient`` is specified, the 2 criteria prefixed with “[default]” are not |
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321 applied. |
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322 |
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323 If ``--allow-unaffected`` is specified, the criterion prefixed with |
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324 “[affected]” is not enforced. |
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325 |
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326 ---- |
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327 |
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328 *Autosomal dominant* |
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329 |
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330 Criteria: |
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331 |
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332 - All affecteds must be het |
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333 - [affected] No unaffected can be het or homalt (can be unknown) |
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334 - de_novo mutations are not auto_dom (at least not in the first generation) |
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335 - At least 1 affected must have 1 affected parent (or have no parents). |
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336 - If no affected has a parent, a warning is issued. |
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337 - [default] All affecteds must have parents with known phenotype. |
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338 - [default] All affected kids must have at least 1 affected parent |
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339 |
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changeset
|
340 If ``--lenient`` is specified, the criteria prefixed with “[default]” are not |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
341 enforced. |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
342 |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
343 If ``--allow-unaffected`` is specified, the criterion prefixed with |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
344 “[affected]” is not enforced. |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
345 |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
346 Note that, for autosomal dominant, ``--lenient`` allows singleton affecteds to |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
347 be used to meet the ``--min-kindreds`` requirement if they are HET. |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
348 |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
349 If there is incomplete penetrance in the kindred (unaffected obligate carriers), |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
350 these individuals currently must be coded as having unknown phenotype or as |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
351 being affected. |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
352 |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
353 ---- |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
354 |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
355 *X-linked recessive* |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
356 |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
357 Criteria: |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
358 |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
359 - Affected females must be HOM_ALT |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
360 - Unaffected females are HET or HOM_REF |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
361 - Affected males are not HOM_REF |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
362 - Unaffected males are HOM_REF |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
363 |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
364 Note: Pseudo-autosomal regions are not accounted for by the tool. |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
365 |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
366 ---- |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
367 |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
368 *X-linked dominant* |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
369 |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
370 Criteria: |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
371 |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
372 - Affected males are HET or HOM_ALT |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
373 - Affected females must be HET |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
374 - Unaffecteds must be HOM_REF |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
375 - girls of affected dad must be affected |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
376 - boys of affected dad must be unaffected |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
377 - mothers of affected males must be het (and affected) |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
378 - at least 1 parent of affected females must be het (and affected). |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
379 |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
380 Note: Pseudo-autosomal regions are not accounted for by the tool. |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
381 |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
382 ---- |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
383 |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
384 *De-novo mutations* |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
385 |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
386 Criteria: |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
387 |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
388 - all affected must be het |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
389 - [affected] all unaffected must be homref or homalt |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
390 - at least 1 affected kid must have unaffected parents |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
391 - [default] if an affected has affected parents, it’s not de_novo |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
392 - [default] all affected kids must have unaffected (or no) parents |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
393 - [default] warning if none of the affected samples have parents. |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
394 |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
395 The last 3 items, prefixed with [default] can be turned off with ``--lenient``. |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
396 |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
397 If ``--allow-unaffected`` is specified, then the criterion prefixed [affected] |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
398 is not enforced. |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
399 |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
400 ---- |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
401 |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
402 *X-linked de-novo mutations* |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
403 |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
404 Criteria: |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
405 |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
406 - affected female child must be het |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
407 - affected male child must be hom_alt (or het) |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
408 - parents should be unaffected and hom_ref |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
409 |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
410 Note: Pseudo-autosomal regions are not accounted for by the tool. |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
411 |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
412 ---- |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
413 |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
414 *Compound heterozygosity* |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
415 |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
416 Unlike canonical recessive sites where the same recessive allele is inherited |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
417 from both parents at the *same* site in the gene, compound heterozygosity |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
418 occurs when the individual’s phenotype is caused by two heterozygous recessive |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
419 alleles at *different* sites in a particular gene. |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
420 |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
421 To detect compound heterozygosity, the tool looks for two heterozygous variants |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
422 impacting the same gene at different loci. The complicating factor is that this |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
423 is a case of *recessive* inheritance and as such, we must also require that the |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
424 consequential alleles at each heterozygous site were inherited on different |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
425 chromosomes (one from each parent). Hence, where possible, the tool will phase |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
426 by transmission. |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
427 |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
428 Criteria (default): |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
429 |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
430 - All affected individuals must be heterozygous at both sites. |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
431 - No unaffected can be homozygous alterate at either site. |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
432 - Neither parent of an affected sample can be homozygous reference at both |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
433 sites. |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
434 - If any unphased-unaffected is het at both sites, the site will be given lower |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
435 priority. |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
436 - No phased-unaffected can be heterozygous at both sites. |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
437 |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
438 a. ``--allow-unaffected`` keeps sites where a phased unaffected shares the |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
439 het-pair |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
440 b. unphased, unaffected that share the het pair are counted and reported for |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
441 each candidate pair. |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
442 - Candidates where an affected from the same family does NOT share the same het |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
443 pair are removed. |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
444 - Sites are automatically phased by transmission when parents are present in |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
445 order to remove false positive candidates. |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
446 |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
447 If data from one or both parents are unavailable and the child’s data was not |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
448 phased prior to loading into GEMINI, all comp_het variant pairs will |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
449 automatically be given at most priority == 2. If there’s only a single parent |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
450 and both the parent and the affected are HET at both sites, the candidate |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
451 will have priority 3. |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
452 |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
453 Criteria (``--pattern-only``): |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
454 |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
455 - Kid must be HET at both sites. |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
456 - Kid must have alts on different chromosomes. |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
457 - Neither parent can be HOM_ALT at either site. |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
458 - If either parent is phased at both sites and matches the kid, it’s excluded. |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
459 - When the above criteria are met, and both parents and kid are phased or |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
460 parents are HET at different sites, the priority is 1. |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
461 - If either parent is HET at both sites, priority is reduced. |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
462 - If both parents are not phased, the priority is 2. |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
463 - For every parent that’s a het at both sites, the priority is incremented by 1. |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
464 - The priority in a family is the minimum found among all kids. |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
465 |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
466 ---- |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
467 |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
468 *Violation of Mendelian laws* |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
469 |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
470 The tool can be used to detect the following kinds of non-Mendelian patterns: |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
471 |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
472 - loss of heterozygosity (LOH) events |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
473 - de-novo mutations |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
474 - implausible de-novo mutations |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
475 - potential cases of uniparental disomy |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
476 |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
477 Criteria: |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
478 |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
479 - LOH: child and one parent are opposite homozygotes; other parent is HET |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
480 - plausible de novo: kid is het. parents are same homozygotes |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
481 - implausible de novo: kid is homozygote. parents are same homozygotes and opposite to kid. |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
482 - uniparental disomy: parents are opposite homozygotes; kid is homozygote |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
483 |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
484 ]]> |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
485 </help> |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
486 <expand macro="citations"/> |
3123ce7acd0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents:
diff
changeset
|
487 </tool> |