|
0
|
1 <tool id="cga_snpdiff" name="snpdiff" version="0.0.1">
|
|
|
2
|
|
|
3 <description>compares snp calls to a Complete Genomics variant file.</description> <!--adds description in toolbar-->
|
|
|
4
|
|
|
5 <requirements>
|
|
|
6 <requirement type="binary">cgatools</requirement>
|
|
|
7 </requirements>
|
|
|
8
|
|
|
9 <command> <!--run executable-->
|
|
|
10 cgatools snpdiff --beta -h
|
|
|
11 </command>
|
|
|
12
|
|
|
13 <outputs>
|
|
|
14 <data format="tabular" name="output" />
|
|
|
15 </outputs>
|
|
|
16
|
|
|
17 <inputs>
|
|
|
18 </inputs>
|
|
|
19
|
|
|
20 <help>
|
|
|
21
|
|
|
22 **What it does**
|
|
|
23
|
|
|
24 This tool ompares snp calls to a Complete Genomics variant file.
|
|
|
25
|
|
|
26 cgatools: http://sourceforge.net/projects/cgatools/files/
|
|
|
27
|
|
|
28 -----
|
|
|
29
|
|
|
30 **cgatools Manual**::
|
|
|
31
|
|
|
32 COMMAND NAME
|
|
|
33 snpdiff - Compares snp calls to a Complete Genomics variant file.
|
|
|
34
|
|
|
35 DESCRIPTION
|
|
|
36 Compares the snp calls in the "genotypes" file to the calls in a Complete
|
|
|
37 Genomics variant file. The genotypes file is a tab-delimited file with at
|
|
|
38 least the following columns (additional columns may be given):
|
|
|
39
|
|
|
40 Chromosome (Required) The name of the chromosome.
|
|
|
41 Offset0Based (Required) The 0-based offset in the chromosome.
|
|
|
42 GenotypesStrand (Optional) The strand of the calls in the Genotypes
|
|
|
43 column (+ or -, defaults to +).
|
|
|
44 Genotypes (Optional) The calls, one per allele. The following
|
|
|
45 calls are recognized:
|
|
|
46 A,C,G,T A called base.
|
|
|
47 N A no-call.
|
|
|
48 - A deleted base.
|
|
|
49 . A non-snp variation.
|
|
|
50
|
|
|
51 The output is a tab-delimited file consisting of the columns of the
|
|
|
52 original genotypes file, plus the following additional columns:
|
|
|
53
|
|
|
54 Reference The reference base at the given position.
|
|
|
55 VariantFile The calls made by the variant file, one per allele.
|
|
|
56 The character codes are the same as is described for
|
|
|
57 the Genotypes column.
|
|
|
58 DiscordantAlleles (Only if Genotypes is present) The number of
|
|
|
59 Genotypes alleles that are discordant with calls in
|
|
|
60 the VariantFile. If the VariantFile is described as
|
|
|
61 haploid at the given position but the Genotypes is
|
|
|
62 diploid, then each genotype allele is compared
|
|
|
63 against the haploid call of the VariantFile.
|
|
|
64 NoCallAlleles (Only if Genotypes is present) The number of
|
|
|
65 Genotypes alleles that were no-called by the
|
|
|
66 VariantFile. If the VariantFile is described as
|
|
|
67 haploid at the given position but the Genotypes is
|
|
|
68 diploid, then a VariantFile no-call is counted twice.
|
|
|
69
|
|
|
70 The verbose output is a tab-delimited file consisting of the columns of the
|
|
|
71 original genotypes file, plus the following additional columns:
|
|
|
72
|
|
|
73 Reference The reference base at the given position.
|
|
|
74 VariantFile The call made by the variant file for one allele (there is
|
|
|
75 a line in this file for each allele). The character codes
|
|
|
76 are the same as is described for the Genotypes column.
|
|
|
77 [CALLS] The rest of the columns are pasted in from the VariantFile,
|
|
|
78 describing the variant file line used to make the call.
|
|
|
79
|
|
|
80 The stats output is a comma-separated file with several tables describing
|
|
|
81 the results of the snp comparison, for each diploid genotype. The tables
|
|
|
82 all describe the comparison result (column headers) versus the genotype
|
|
|
83 classification (row labels) in different ways. The "Locus classification"
|
|
|
84 tables have the most detailed match classifications, while the "Locus
|
|
|
85 concordance" tables roll these match classifications up into "discordance"
|
|
|
86 and "no-call". A locus is considered discordant if it is discordant for
|
|
|
87 either allele. A locus is considered no-call if it is concordant for both
|
|
|
88 alleles but has a no-call on either allele. The "Allele concordance"
|
|
|
89 describes the comparison result on a per-allele basis.
|
|
|
90
|
|
|
91 OPTIONS
|
|
|
92 -h [ --help ]
|
|
|
93 Print this help message.
|
|
|
94
|
|
|
95 --reference arg
|
|
|
96 The input crr file.
|
|
|
97
|
|
|
98 --variants arg
|
|
|
99 The input variant file.
|
|
|
100
|
|
|
101 --genotypes arg
|
|
|
102 The input genotypes file.
|
|
|
103
|
|
|
104 --output-prefix arg
|
|
|
105 The path prefix for all output reports.
|
|
|
106
|
|
|
107 --reports arg (=Output,Verbose,Stats)
|
|
|
108 Comma-separated list of reports to generate. A report is one of:
|
|
|
109 Output The output genotypes file.
|
|
|
110 Verbose The verbose output file.
|
|
|
111 Stats The stats output file.
|
|
|
112
|
|
|
113 SUPPORTED FORMAT_VERSION
|
|
|
114 0.3 or later
|
|
|
115 </help>
|
|
|
116 </tool>
|
