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comparison gemini_roh.xml @ 17:65f742e605ec draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 344140b8df53b8b7024618bb04594607a045c03a
author iuc
date Mon, 04 May 2015 22:46:38 -0400
parents 53a5647e5271
children ce61d4876838
comparison
equal deleted inserted replaced
16:ae03de7a9fee 17:65f742e605ec
1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0"> 1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0">
2 <description>Identifying runs of homozygosity</description> 2 <description>Identifying runs of homozygosity</description>
3 <expand macro="requirements" />
4 <expand macro="version_command" />
5 <macros> 3 <macros>
6 <import>gemini_macros.xml</import> 4 <import>gemini_macros.xml</import>
7 <token name="@BINARY@">roh</token> 5 <token name="@BINARY@">roh</token>
8 </macros> 6 </macros>
7 <expand macro="requirements" />
8 <expand macro="stdio" />
9 <expand macro="version_command" />
9 <command> 10 <command>
10 <![CDATA[ 11 <![CDATA[
11 gemini @BINARY@ 12 gemini @BINARY@
12 --min-snps $min_snps 13 --min-snps $min_snps
13 --min-total-depth $min_total_depth 14 --min-total-depth $min_total_depth
20 #end if 21 #end if
21 "${ infile }" 22 "${ infile }"
22 > "${ outfile }" 23 > "${ outfile }"
23 ]]> 24 ]]>
24 </command> 25 </command>
25 <expand macro="stdio" />
26 <inputs> 26 <inputs>
27 <expand macro="infile" /> 27 <expand macro="infile" />
28 28
29 <param name="min_snps" type="integer" value="25" size="5" label="Minimum number of expected homozygous SNPs" help="default: 25 (--min-snps)"> 29 <param name="min_snps" type="integer" value="25" size="5" label="Minimum number of expected homozygous SNPs" help="default: 25 (--min-snps)">
30 <validator type="in_range" min="0"/> 30 <validator type="in_range" min="0"/>
31 </param> 31 </param>
32 <param name="min_total_depth" type="integer" value="20" size="10" label="The minimum overall sequencing depth requiredfor a SNP to be considered" help="default: 20 (--min-total-depth)"> 32 <param name="min_total_depth" type="integer" value="20" size="10" label="The minimum overall sequencing depth requiredfor a SNP to be considered" help="default: 20 (--min-total-depth)">
33 <validator type="in_range" min="0"/> 33 <validator type="in_range" min="0"/>
34 </param> 34 </param>
35 <param name="min_gt_depth" type="integer" value="0" size="10" label="The minimum required sequencing depth underlying a given sample's genotype for a SNP to be considered" 35 <param name="min_gt_depth" type="integer" value="0" size="10" label="The minimum required sequencing depth underlying a given sample's genotype for a SNP to be considered"
36 help="default: 0 (--min-gt-depth)"> 36 help="default: 0 (--min-gt-depth)">
37 <validator type="in_range" min="0"/> 37 <validator type="in_range" min="0"/>
38 </param> 38 </param>
39 <param name="min_size" type="integer" value="100000" size="10" label="Minimum run size in base pairs" help="default: 100000 (--min-size)"> 39 <param name="min_size" type="integer" value="100000" size="10" label="Minimum run size in base pairs" help="default: 100000 (--min-size)">
40 <validator type="in_range" min="1"/> 40 <validator type="in_range" min="1"/>
64 =========================================================================== 64 ===========================================================================
65 ``ROH``: Identifying runs of homozygosity 65 ``ROH``: Identifying runs of homozygosity
66 =========================================================================== 66 ===========================================================================
67 Runs of homozygosity are long stretches of homozygous genotypes that reflect 67 Runs of homozygosity are long stretches of homozygous genotypes that reflect
68 segments shared identically by descent and are a result of consanguinity or 68 segments shared identically by descent and are a result of consanguinity or
69 natural selection. Consanguinity elevates the occurrence of rare recessive 69 natural selection. Consanguinity elevates the occurrence of rare recessive
70 diseases (e.g. cystic fibrosis) that represent homozygotes for strongly deleterious 70 diseases (e.g. cystic fibrosis) that represent homozygotes for strongly deleterious
71 mutations. Hence, the identification of these runs holds medical value. 71 mutations. Hence, the identification of these runs holds medical value.
72 72
73 The 'roh' tool in GEMINI returns runs of homozygosity identified in whole genome data. 73 The 'roh' tool in GEMINI returns runs of homozygosity identified in whole genome data.
74 The tool basically looks at every homozygous position on the chromosome as a possible 74 The tool basically looks at every homozygous position on the chromosome as a possible
75 start site for the run and looks for those that could give rise to a potentially long 75 start site for the run and looks for those that could give rise to a potentially long
76 stretch of homozygous genotypes. 76 stretch of homozygous genotypes.
77 77
78 For e.g. for the given example allowing ``1 HET`` genotype (h) and ``2 UKW`` genotypes (u) 78 For e.g. for the given example allowing ``1 HET`` genotype (h) and ``2 UKW`` genotypes (u)
79 the possible roh runs (H) would be: 79 the possible roh runs (H) would be:
80 80
81 81
82 :: 82 ::
83 83
88 roh_run4 = H H H H H H H h H H H H H 88 roh_run4 = H H H H H H H h H H H H H
89 89
90 roh returned for --min-snps = 20 would be: 90 roh returned for --min-snps = 20 would be:
91 91
92 :: 92 ::
93 93
94 roh_run1 = H H H H h H H H H u H H H H H u H H H H H H H 94 roh_run1 = H H H H h H H H H u H H H H H u H H H H H H H
95 roh_run2 = H H H H u H H H H H u H H H H H H H h H H H H H 95 roh_run2 = H H H H u H H H H H u H H H H H H H h H H H H H
96 96
97 97
98 As you can see, the immediate homozygous position right of a break (h or u) would be the possible 98 As you can see, the immediate homozygous position right of a break (h or u) would be the possible
99 start of a new roh run and genotypes to the left of a break are pruned since they cannot 99 start of a new roh run and genotypes to the left of a break are pruned since they cannot
100 be part of a longer run than we have seen before. 100 be part of a longer run than we have seen before.
101 101
102 102
103 @CITATION@ 103 @CITATION@
104 </help> 104 </help>