Mercurial > repos > iuc > gemini

comparison gemini_roh.xml @ 0:14caa57eca63 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author iuc
date Mon, 11 Aug 2014 07:44:30 -0400
parents
children e6512af21622
comparison
equal deleted inserted replaced
-1:000000000000 0:14caa57eca63
1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0">
2 <description>Identifying runs of homozygosity</description>
3 <expand macro="requirements" />
4 <expand macro="version_command" />
5 <macros>
6 <import>gemini_macros.xml</import>
7 <token name="@BINARY@">roh</token>
8 </macros>
9 <command>
10 <![CDATA[
11 gemini @BINARY@
12 --min-snps $min_snps
13 --min-total-depth $min_total_depth
14 --min-gt-depth $min_gt_depth
15 --min-size $min_size
16 --max-hets §max_hets
17 --max-unknowns $max_unknowns
18 -s $samples
19 "${ infile }"
20 -> "${ outfile }"
21 ]]>
22 </command>
23 <expand macro="stdio" />
24 <inputs>
25 <param name="infile" type="data" format="sqlite" label="GEMINI database" />
26
27 <param name="min_snps" type="integer" value="25" size="5" label="Minimum number of expected homozygous SNPs" help="default: 25 (--min-snps)">
28 <validator type="in_range" min="0"/>
29 </param>
30 <param name="min_total_depth" type="integer" value="20" size="10" label="The minimum overall sequencing depth requiredfor a SNP to be considered" help="default: 20 (--min-total-depth)">
31 <validator type="in_range" min="0"/>
32 </param>
33 <param name="min_gt_depth" type="integer" value="0" size="10" label="The minimum required sequencing depth underlying a given sample's genotype for a SNP to be considered"
34 help="default: 0 (--min-gt-depth)">
35 <validator type="in_range" min="0"/>
36 </param>
37 <param name="min_size" type="integer" value="100000" size="10" label="Minimum run size in base pairs" help="default: 100000 (--min-size)">
38 <validator type="in_range" min="1"/>
39 </param>
40 <param name="max_hets" type="integer" value="1" size="5" label="Maximum number of allowed hets in the run" help="default: 1 (--max-hets)">
41 <validator type="in_range" min="1"/>
42 </param>
43 <param name="max_unknowns" type="integer" value="3" size="5" label="Maximum number of allowed unknowns in the run" help="default: 3 (-max-unknowns)">
44 <validator type="in_range" min="0"/>
45 </param>
46
47 <param name="samples" size="30" type="text" value="" label="Comma separated list of samples to screen for ROHs" help="e.g S120,S450 (-s)"/>
48
49 </inputs>
50
51 <outputs>
52 <data name="outfile" format="tabular" label="${tool.name} on ${on_string}" />
53 </outputs>
54 <tests>
55 <test>
56 </test>
57 </tests>
58 <help>
59
60 **What it does**
61
62 ===========================================================================
63 ``ROH``: Identifying runs of homozygosity
64 ===========================================================================
65 Runs of homozygosity are long stretches of homozygous genotypes that reflect
66 segments shared identically by descent and are a result of consanguinity or
67 natural selection. Consanguinity elevates the occurrence of rare recessive
68 diseases (e.g. cystic fibrosis) that represent homozygotes for strongly deleterious
69 mutations. Hence, the identification of these runs holds medical value.
70
71 The 'roh' tool in GEMINI returns runs of homozygosity identified in whole genome data.
72 The tool basically looks at every homozygous position on the chromosome as a possible
73 start site for the run and looks for those that could give rise to a potentially long
74 stretch of homozygous genotypes.
75
76 For e.g. for the given example allowing ``1 HET`` genotype (h) and ``2 UKW`` genotypes (u)
77 the possible roh runs (H) would be:
78
79
80 ::
81
82 genotype_run = H H H H h H H H H u H H H H H u H H H H H H H h H H H H H h H H H H H
83 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
84 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
85 roh_run3 = H H H H H u H H H H H H H h H H H H H
86 roh_run4 = H H H H H H H h H H H H H
87
88 roh returned for --min-snps = 20 would be:
89
90 ::
91
92 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
93 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
94
95
96 As you can see, the immediate homozygous position right of a break (h or u) would be the possible
97 start of a new roh run and genotypes to the left of a break are pruned since they cannot
98 be part of a longer run than we have seen before.
99
100
101 @CITATION@
102 </help>
103 <expand macro="citations"/>
104 </tool>