Mercurial > repos > bgruening > vt_decompose

annotate vt_decompose.xml @ 0:490e605d1f44 draft default tip

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author bgruening
date Sat, 04 Jun 2016 12:45:04 -0400
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1 <tool id="vt_decompose" name="VT @BINARY@" version="@VERSION@.0">
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2 <description>decomposes multiallelic variants into biallelic ones</description>
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3 <macros>
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4 <import>vt_macros.xml</import>
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5 <token name="@BINARY@">decompose</token>
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6 </macros>
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7 <expand macro="requirements" />
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8 <expand macro="stdio" />
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9 <expand macro="version_command" />
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10 <command>
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11 <![CDATA[
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12
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13 ln -s "${ infile }" infile.vcf &&
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14
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15
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16 vt @BINARY@
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17 #if str($output_format) == 'bcf':
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18 -o decompose.bcf
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19 #else:
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20 -o decompose.vcf
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21 #end if
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22 $s
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23 infile.vcf
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24
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25 &&
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26 ## For some reason, the file move will randomly produce empty files.
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27 ## Wait two seconds to let the system close file handlers and clean up.
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28 sleep 2
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29 &&
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30
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31 #if str($output_format) == 'bcf':
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32 mv decompose.bcf "${ outfile }";
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33 #else:
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34 mv decompose.vcf "${ outfile }";
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35 #end if
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36
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37 ]]>
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38 </command>
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39 <inputs>
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40 <param name="infile" type="data" format="vcf" label="VCF file to be normalised" />
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41
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42 <param argument="-s" type="boolean" truevalue="-s" falsevalue=""
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43 selected="false" label="Smart decomposition"
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44 help="Splits up INFO and GENOTYPE fields that have number counts of R and A appropriately."/>
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45
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46 <param name="output_format" type="select" label="Choose the output format" help="">
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47 <option value="bcf">BCF</option>
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48 <option value="vcf" selected="true">VCF</option>
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49 </param>
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50 </inputs>
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51 <outputs>
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52 <data name="outfile" format="vcf" label="${tool.name} on ${on_string}">
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53 <change_format>
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54 <when input="output_format" value="bcf" format="bcf" />
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55 </change_format>
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56 </data>
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57 </outputs>
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58 <tests>
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59 <test>
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60 <param name="infile" value="infile01.vcf" />
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61 <output name="outfile" file="decompose_result01.vcf" ftype="vcf" />
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62 </test>
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63 <test>
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64 <param name="infile" value="infile02.vcf" />
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65 <param name="s" value="True" />
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66 <output name="outfile" file="decompose_result02.vcf" ftype="vcf" />
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67 </test>
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68 </tests>
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69 <help>
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70 <![CDATA[
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71
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72 **What it does**
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73
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74 Decompose multiallelic variants in a VCF file.
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75 If the VCF file has genotype fields GT,PL, GL or DP, they are modified to reflect the change in alleles.
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76 All other genotype fields are removed. The -s option will retain the fields and decompose fields of counts R and A accordingingly.
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77
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78 Decomposition and combining variants is a complex operation where the correctness is dependent on:
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79
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80 * whether the observed variants are seen in the same sample
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81 * if same sample, whether they are homozygous or heterozygous
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82 * if both heterozygous, whether they are in the same haplotype or not (if known)
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83
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84 and one should be aware of the issues in handling variants resulting from such operations.
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85 The original purpose of this tool is to allow for allelic comparisons between call sets.
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86
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87 Standard option:
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88
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89 Before decomposition
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90
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91 .. code::
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92
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93 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT S1 S2
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94 1 3759889 . TA TAA,TAAA,T . PASS AF=0.342,0.173,0.037 GT:DP:PL 1/2:81:281,5,9,58,0,115,338,46,116,809 0/0:86:0,30,323,31,365,483,38,291,325,567
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95
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96 After decomposition
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97
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98 .. code::
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99
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100 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT S1 S2
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101 1 3759889 . TA TAA . PASS OLD_MULTIALLELIC=1:3759889:TA/TAA/TAAA/T GT:PL 1/.:281,5,9 0/0:0,30,323
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102 1 3759889 . TA TAAA . . OLD_MULTIALLELIC=1:3759889:TA/TAA/TAAA/T GT:PL ./1:281,58,115 0/0:0,31,483
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103 1 3759889 . TA T . . OLD_MULTIALLELIC=1:3759889:TA/TAA/TAAA/T GT:PL ./.:281,338,809 0/0:0,38,567
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104
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105
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106 One might want to post process the partial genotypes like 1/. to the best guess genotype based on the PL values.
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107
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108
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109 With **-s** option:
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110
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111 Before decomposition
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112
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113 .. code::
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114
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115 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT S1 S2
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116 1 3759889 . TA TAA,TAAA,T . PASS AF=0.342,0.173,0.037 GT:DP:PL 1/2:81:281,5,9,58,0,115,338,46,116,809 0/0:86:0,30,323,31,365,483,38,291,325,567
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117
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118 After decomposition
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119
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120 .. code::
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121
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122 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT S1 S2
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123 1 3759889 . TA TAA . PASS AF=0.342;OLD_MULTIALLELIC=1:3759889:TA/TAA/TAAA/T GT:PL 1/.:281,5,9 0/0:0,30,323
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124 1 3759889 . TA TAAA . . AF=0.173;OLD_MULTIALLELIC=1:3759889:TA/TAA/TAAA/T GT:PL ./1:281,58,115 0/0:0,31,483
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125 1 3759889 . TA T . . AF=0.037;OLD_MULTIALLELIC=1:3759889:TA/TAA/TAAA/T GT:PL ./.:281,338,809 0/0:0,38,567
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126
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127 In general, you should recompute fields that involves alleles after decomposition. Information is generally lost after vertically decomposing a variant, so care should be taken in interpreting the resultant values.
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128
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129 @CITATION@
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130 ]]>
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131 </help>
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132 <expand macro="citations"/>
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133 </tool>