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1 <tool id="snpSift_extractFields" name="SnpSift Extract Fields" version="@WRAPPER_VERSION@.0">
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2 <options sanitize="False" />
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3 <description>from a VCF file inot a tabular file</description>
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4 <macros>
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5 <import>snpSift_macros.xml</import>
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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><![CDATA[
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11 cat "$input"
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12 #if $one_effect_per_line:
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13 | \$SNPEFF_JAR_PATH/scripts/vcfEffOnePerLine.pl
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14 #end if
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15 | java -Xmx6G -jar \$SNPEFF_JAR_PATH/SnpSift.jar extractFields
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16 #if $separator:
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17 -s '$separator'
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18 #end if
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19 #if $empty_text:
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20 -e '$empty_text'
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21 #end if
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22 -
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23 #echo ' '.join(['"%s"' % x for x in $extract.split()])
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24 > $output
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25 ]]>
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26 </command>
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27 <inputs>
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28 <param format="vcf" name="input" type="data" label="Variant input file in VCF format"/>
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29 <param name="extract" type="text" label="Extract" size="160" help="Need help? See below a few examples." />
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30 <param name="one_effect_per_line" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="One effect per line" help="When variants have more than one effect, lists one effect per line, while all other parameters in the line are repeated across mutiple lines" />
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31 <param name="separator" type="text" value="" optional="true" label="multiple field separator" size="1" help="Separate multiple fields in one column with this character, e.g. a comma, rather than a column for each of the multiple values">
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32 </param>
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33 <param name="empty_text" type="text" value="" optional="true" label="empty field text" size="10" help="Represent empty fields with this value, rather than leaving them blank" >
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34 </param>
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35 </inputs>
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36 <outputs>
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37 <data format="tabular" name="output" />
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38 </outputs>
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39 <tests>
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40 <test>
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41 <param name="input" ftype="vcf" value="test_rmInfo.vcf"/>
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42 <param name="extract" value="CHROM POS REF ALT EFF[*].EFFECT"/>
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43 <output name="output">
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44 <assert_contents>
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45 <has_text text="INTRAGENIC" />
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46 <not_has_text text="DOWNSTREAM,INTRAGENIC,INTRON,UTR_3_PRIME" />
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47 </assert_contents>
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48 </output>
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49 </test>
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50
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51 <test>
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52 <param name="input" ftype="vcf" value="test_rmInfo.vcf"/>
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53 <param name="extract" value="CHROM POS REF ALT EFF[*].EFFECT"/>
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54 <param name="separator" value=","/>
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55 <output name="output">
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56 <assert_contents>
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57 <has_text text="DOWNSTREAM,INTRAGENIC,INTRON,UTR_3_PRIME" />
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58 </assert_contents>
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59 </output>
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60 </test>
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61
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62 </tests>
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63 <help><![CDATA[
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64
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65 **SnpSift Extract Fields**
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66
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67 Extract fields from a VCF file to a TXT, tab separated format, that you can easily load in R, XLS, etc.
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68
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69 http://snpeff.sourceforge.net/SnpSift.html#Extract
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70
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71 You can also use sub-fields and genotype fields / sub-fields such as:
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72
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73 ::
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74
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75 Standard VCF fields:
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76 CHROM
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77 POS
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78 ID
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79 REF
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80 ALT
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81 FILTER
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82 INFO fields:
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83 AF
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84 AC
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85 DP
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86 MQ
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87 etc. (any info field available)
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88 SnpEff 'ANN' fields:
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89 "ANN[*].ALLELE" (alias GENOTYPE)
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90 "ANN[*].EFFECT" (alias ANNOTATION): Effect in Sequence ontology terms (e.g. 'missense_variant', 'synonymous_variant', 'stop_gained', etc.)
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91 "ANN[*].IMPACT:" { HIGH, MODERATE, LOW, MODIFIER }
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92 "ANN[*].GENE:" Gene name (e.g. 'PSD3')
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93 "ANN[*].GENEID:" Gene ID
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94 "ANN[*].FEATURE
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95 " ANN[*].FEATUREID (alias TRID: Transcript ID)
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96 "ANN[*].BIOTYPE:" Biotype, as described by the annotations (e.g. 'protein_coding')
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97 "ANN[*].RANK:" Exon or Intron rank (i.e. exon number in a transcript)
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98 "ANN[*].HGVS_C" (alias HGVS_DNA, CODON): Variant in HGVS (DNA) notation
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99 "ANN[*].HGVS_P" (alias HGVS, HGVS_PROT, AA): Variant in HGVS (protein) notation
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100 "ANN[*].CDNA_POS" (alias POS_CDNA)
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101 "ANN[*].CDNA_LEN" (alias LEN_CDNA)
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102 "ANN[*].CDS_POS" (alias POS_CDS)
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103 "ANN[*].CDS_LEN" (alias LEN_CDS)
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104 "ANN[*].AA_POS" (alias POS_AA)
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105 "ANN[*].AA_LEN" (alias LEN_AA)
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106 "ANN[*].DISTANCE"
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107 "ANN[*].ERRORS" (alias WARNING, INFOS)
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108 SnpEff 'EFF' fields (this is for older SnpEff/SnpSift versions, new version use 'ANN' field):
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109 "EFF[*].EFFECT"
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110 "EFF[*].IMPACT"
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111 "EFF[*].FUNCLASS"
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112 "EFF[*].CODON"
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113 "EFF[*].AA"
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114 "EFF[*].AA_LEN"
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115 "EFF[*].GENE"
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116 "EFF[*].BIOTYPE"
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117 "EFF[*].CODING"
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118 "EFF[*].TRID"
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119 "EFF[*].RANK"
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120 SnpEff 'LOF' fields:
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121 "LOF[*].GENE"
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122 "LOF[*].GENEID"
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123 "LOF[*].NUMTR"
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124 "LOF[*].PERC"
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125 SnpEff' NMD' fields:
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126 "NMD[*].GENE"
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127 "NMD[*].GENEID"
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128 "NMD[*].NUMTR"
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129 "NMD[*].PERC"
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130
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131
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132 Some examples:
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133
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134 - *Extracting chromosome, position, ID and allele frequency from a VCF file:*
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135
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136 **CHROM POS ID AF**
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137
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138 The result will look something like:
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139
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140 ::
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141
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142 #CHROM POS ID AF
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143 1 69134 0.086
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144 1 69496 rs150690004 0.001
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145
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146
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147 - *Extracting genotype fields:*
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148
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149 **CHROM POS ID THETA GEN[0].GL[1] GEN[1].GL GEN[3].GL[*] GEN[*].GT**
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150
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151 This means to extract:
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152
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153 - CHROM POS ID: regular fields (as in the previous example)
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154 - THETA : This one is from INFO
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155 - GEN[0].GL[1] : Second likelihood from first genotype
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156 - GEN[1].GL : The whole GL fiels (all entries without separating them)
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157 - GEN[3].GL[*] : All likelihoods form genotype 3 (this time they will be tab separated, as opposed to the previous one).
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158 - GEN[*].GT : Genotype subfields (GT) from ALL samples (tab separated).
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159
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160 The result will look something like:
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161
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162 ::
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163
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164 #CHROM POS ID THETA GEN[0].GL[1] GEN[1].GL GEN[3].GL[*] GEN[*].GT
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165 1 10583 rs58108140 0.0046 -0.47 -0.24,-0.44,-1.16 -0.48 -0.48 -0.48 0|0 0|0 0|0 0|1 0|0 0|1 0|0 0|0 0|1
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166 1 10611 rs189107123 0.0077 -0.48 -0.24,-0.44,-1.16 -0.48 -0.48 -0.48 0|0 0|1 0|0 0|0 0|0 0|0 0|0 0|0 0|0
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167 1 13302 rs180734498 0.0048 -0.58 -2.45,-0.00,-5.00 -0.48 -0.48 -0.48 0|0 0|1 0|0 0|0 0|0 1|0 0|0 0|1 0|0
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168
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169 - *Extracting fields with multiple values:*
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170 (notice that there are multiple effect columns per line because there are mutiple effects per variant)
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171
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172 **CHROM POS REF ALT ANN[*].EFFECT**
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173
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174 The result will look something like:
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175
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176 ::
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177
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178 #CHROM POS REF ALT ANN[*].EFFECT
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179 22 17071756 T C 3_prime_UTR_variant downstream_gene_variant
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180 22 17072035 C T missense_variant downstream_gene_variant
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181 22 17072258 C A missense_variant downstream_gene_variant
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182
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183 - *Extracting fields with multiple values using a comma as a multipe field separator:*
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184
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185 **CHROM POS REF ALT ANN[*].EFFECT ANN[*].HGVS_P**
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186
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187 The result will look something like:
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188
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189 ::
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190
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191 #CHROM POS REF ALT ANN[*].EFFECT ANN[*].HGVS_P
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192 22 17071756 T C 3_prime_UTR_variant,downstream_gene_variant .,.
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193 22 17072035 C T missense_variant,downstream_gene_variant p.Gly469Glu,.
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194 22 17072258 C A missense_variant,downstream_gene_variant p.Gly395Cys,.
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195
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196
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197 - *Extracting fields with multiple values, one effect per line:*
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198
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199 **CHROM POS REF ALT ANN[*].EFFECT**
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200
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201 The result will look something like:
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202
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203 ::
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204
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205 #CHROM POS REF ALT ANN[*].EFFECT
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206 22 17071756 T C 3_prime_UTR_variant
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207 22 17071756 T C downstream_gene_variant
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208 22 17072035 C T missense_variant
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209 22 17072035 C T downstream_gene_variant
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210 22 17072258 C A missense_variant
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211 22 17072258 C A downstream_gene_variant
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212
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213
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214 @EXTERNAL_DOCUMENTATION@
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215 http://snpeff.sourceforge.net/SnpSift.html#Extract
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216
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217 @CITATION_SECTION@
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218
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219 ]]>
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220 </help>
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221 </tool>
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