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