Mercurial > repos > iuc > snpsift_dbnsfp

annotate snpSift_dbnsfp.xml @ 280:2c41c1631d1c draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5
author iuc
date Mon, 12 Jun 2017 10:24:50 -0400
parents 02f54bf45aaf
children
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280
2c41c1631d1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5
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1 <tool id="snpSift_dbnsfp" name="SnpSift dbNSFP" version="@WRAPPER_VERSION@.0">
2c41c1631d1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5
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2 <description>Add annotations from dbNSFP or similar annotation DBs</description>
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3 <macros>
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4 <import>snpSift_macros.xml</import>
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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5 </macros>
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6 <expand macro="requirements" />
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7 <expand macro="stdio" />
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8 <expand macro="version_command" />
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9 <command><![CDATA[
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10 SnpSift -Xmx6G dbnsfp -v
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11 #if $db.dbsrc == 'cached':
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12 -db '$db.dbnsfp'
2c41c1631d1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5
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13 #if $db.annotations and str($db.annotations) != '':
2c41c1631d1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5
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14 -f '$db.annotations'
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15 #end if
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16 #else:
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17 -db '${db.dbnsfpdb.extra_files_path}/${db.dbnsfpdb.metadata.bgzip}'
2c41c1631d1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5
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18 #if $db.annotations and str($db.annotations) != '':
2c41c1631d1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5
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19 -f '$db.annotations'
2c41c1631d1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5
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20 #end if
2c41c1631d1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5
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21 #end if
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22 '$input' > '$output'
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23 2> tmp.err && grep -v file tmp.err
2c41c1631d1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5
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24 ]]></command>
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25 <inputs>
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26 <param name="input" type="data" format="vcf" label="Variant input file in VCF format"/>
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27 <conditional name="db">
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28 <param name="dbsrc" type="select" label="dbNSFP ">
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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29 <option value="cached">Locally installed dbNSFP database </option>
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30 <option value="history">dbNSFP database from your history</option>
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31 </param>
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32 <when value="cached">
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33 <param name="dbnsfp" type="select" label="Genome">
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34 <options from_data_table="snpsift_dbnsfps">
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35 <column name="name" index="2"/>
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36 <column name="value" index="3"/>
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37 </options>
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38 </param>
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39 <param name="annotations" type="select" multiple="true" display="checkboxes" label="Annotate with">
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40 <options from_data_table="snpsift_dbnsfps">
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41 <column name="name" index="4"/>
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42 <column name="value" index="4"/>
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43 <filter type="param_value" ref="dbnsfp" column="3" />
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44 <filter type="multiple_splitter" column="4" separator=","/>
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45 </options>
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46 </param>
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47 </when>
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48 <when value="history">
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49 <param name="dbnsfpdb" type="data" format="snpsiftdbnsfp" label="DbNSFP"/>
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50 <param name="annotations" type="select" multiple="true" display="checkboxes" label="Annotate with">
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51 <options>
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52 <filter type="data_meta" ref="dbnsfpdb" key="annotation" />
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53 </options>
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54 </param>
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55 </when>
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56 </conditional>
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57 </inputs>
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58 <outputs>
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59 <data name="output" format="vcf" />
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60 </outputs>
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61 <tests>
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62 <!-- This cannot be tested at the moment because test_dbnsfpdb.tabular
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63 is converted from dbnsfp.tabular to snpsiftdbnsfp format on-the-fly
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64 when this tool is run and annotation metadata is not available
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65 until after the conversion is completed.
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66 <test>
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67 <param name="input" ftype="vcf" value="test_annotate_in.vcf"/>
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68 <param name="dbsrc" value="history"/>
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69 <param name="dbnsfpdb" value="test_dbnsfpdb.tabular" ftype="dbnsfp.tabular" />
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70 <param name="annotations" value="aaref,aaalt,genename,aapos,SIFT_score"/>
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71 <output name="output">
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72 <assert_contents>
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73 <has_text text="dbNSFP_SIFT_score=0.15" />
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74 </assert_contents>
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75 </output>
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76 </test> -->
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77 </tests>
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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78 <help><![CDATA[
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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79 The dbNSFP is an integrated database of functional predictions from multiple algorithms (SIFT, Polyphen2, LRT and MutationTaster, PhyloP and GERP++, etc.).
6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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80 It contains variant annotations such as:
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81
280
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82 1000Gp1_AC
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83 Alternative allele counts in the whole 1000 genomes phase 1 (1000Gp1) data
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84 1000Gp1_AF
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85 Alternative allele frequency in the whole 1000Gp1 data
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86 1000Gp1_AFR_AC
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87 Alternative allele counts in the 1000Gp1 African descendent samples
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88 1000Gp1_AFR_AF
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89 Alternative allele frequency in the 1000Gp1 African descendent samples
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90 1000Gp1_AMR_AC
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91 Alternative allele counts in the 1000Gp1 American descendent samples
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92 1000Gp1_AMR_AF
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93 Alternative allele frequency in the 1000Gp1 American descendent samples
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94 1000Gp1_ASN_AC
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95 Alternative allele counts in the 1000Gp1 Asian descendent samples
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96 1000Gp1_ASN_AF
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97 Alternative allele frequency in the 1000Gp1 Asian descendent samples
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98 1000Gp1_EUR_AC
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99 Alternative allele counts in the 1000Gp1 European descendent samples
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100 1000Gp1_EUR_AF
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101 Alternative allele frequency in the 1000Gp1 European descendent samples
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102 aaalt
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103 Alternative amino acid. "." if the variant is a splicing site SNP (2bp on each end of an intron)
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104 aapos
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105 Amino acid position as to the protein. "-1" if the variant is a splicing site SNP (2bp on each end of an intron)
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106 aapos_SIFT
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107 ENSP id and amino acid positions corresponding to SIFT scores. Multiple entries separated by ";"
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108 aapos_FATHMM
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109 ENSP id and amino acid positions corresponding to FATHMM scores. Multiple entries separated by ";"
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110 aaref
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111 Reference amino acid. "." if the variant is a splicing site SNP (2bp on each end of an intron)
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112 alt
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113 Alternative nucleotide allele (as on the + strand)
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114 Ancestral_allele
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115 Ancestral allele (based on 1000 genomes reference data)
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116 cds_strand
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117 Coding sequence (CDS) strand (+ or -)
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118 chr
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119 Chromosome number
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120 codonpos
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121 Position on the codon (1, 2 or 3)
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122 Ensembl_geneid
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123 Ensembl gene ID
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124 Ensembl_transcriptid
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125 Ensembl transcript IDs (separated by ";")
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126 ESP6500_AA_AF
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127 Alternative allele frequency in the African American samples of the NHLBI GO Exome Sequencing Project (ESP6500 data set)
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128 ESP6500_EA_AF
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129 Alternative allele frequency in the European American samples of the NHLBI GO Exome Sequencing Project (ESP6500 data set)
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130 FATHMM_pred
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131 If a FATHMM_score is <=-1.5 (or rankscore <=0.81415) the corresponding non-synonymous SNP is predicted as "D(AMAGING)"; otherwise it is predicted as "T(OLERATED)". Multiple predictions separated by ";"
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132 FATHMM_rankscore
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133 FATHMMori scores were ranked among all FATHMMori scores in dbNSFP. The rankscore is the ratio of the rank of the score over the total number of FATHMMori scores in dbNSFP. If there are multiple scores, only the most damaging (largest) rankscore is presented. The scores range from 0 to 1
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134 FATHMM_score
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135 FATHMM default score (FATHMMori)
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136 fold-degenerate
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137 Degenerate type (0, 2 or 3)
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138 genename
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139 Gene name; if the non-synonymous SNP can be assigned to multiple genes, gene names are separated by ";"
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140 GERP++_NR
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141 GERP++ neutral rate
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142 GERP++_RS
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143 GERP++ RS score, the larger the score, the more conserved the site
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144 GERP++_RS_rankscore
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145 GERP++ RS scores were ranked among all GERP++ RS scores in dbNSFP. The rankscore is the ratio of the rank of the score over the total number of GERP++ RS scores in dbNSFP
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146 hg18_pos(1-coor)
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147 Physical position on the chromosome as to hg18 (1-based coordinate)
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148 Interpro_domain
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149 Domain or conserved site on which the variant locates
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150 LR_pred
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151 Prediction of our LR based ensemble prediction score, "T(olerated)" or "D(amaging)". The score cutoff between "D" and "T" is 0.5. The rankscore cutoff between "D" and "T" is 0.82268
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152 LR_rankscore
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153 LR scores were ranked among all LR scores in dbNSFP. The rankscore is the ratio of the rank of the score over the total number of LR scores in dbNSFP. The scores range from 0 to 1
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154 LR_score
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6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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155 Our logistic regression (LR) based ensemble prediction score, which incorporated 10 scores (SIFT, PolyPhen-2 HDIV, PolyPhen-2 HVAR, GERP++, MutationTaster, Mutation Assessor, FATHMM, LRT, SiPhy, PhyloP) and the maximum frequency observed in the 1000 genomes populations. Larger value means the SNV is more likely to be damaging. Scores range from 0 to 1
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2c41c1631d1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5
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156 LRT_Omega
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157 Estimated nonsynonymous-to-synonymous-rate ratio (Omega, reported by LRT)
280
2c41c1631d1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5
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158 LRT_converted_rankscore
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6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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159 LRTori scores were first converted as LRTnew=1-LRTori*0.5 if Omega<1, or LRTnew=LRTori*0.5 if Omega>=1. Then LRTnew scores were ranked among all LRTnew scores in dbNSFP. The rankscore is the ratio of the rank over the total number of the scores in dbNSFP. The scores range from 0.00166 to 0.85682
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2c41c1631d1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5
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160 LRT_pred
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6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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161 LRT prediction, D(eleterious), N(eutral) or U(nknown), which is not solely determined by the score
280
2c41c1631d1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5
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162 LRT_score
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163 The original LRT two-sided p-value (LRTori), ranges from 0 to 1
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2c41c1631d1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5
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164 MutationAssessor_pred
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165 MutationAssessor's functional impact of a variant
280
2c41c1631d1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5
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166 MutationAssessor_rankscore
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6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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167 MAori scores were ranked among all MAori scores in dbNSFP. The rankscore is the ratio of the rank of the score over the total number of MAori scores in dbNSFP. The scores range from 0 to 1
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2c41c1631d1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5
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168 MutationAssessor_score
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169 MutationAssessor functional impact combined score (MAori)
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170 MutationTaster_converted_rankscore
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171 The MTori scores were first converted: if the prediction is "A" or "D" MTnew=MTori; if the prediction is "N" or "P", MTnew=1-MTori. Then MTnew scores were ranked among all MTnew scores in dbNSFP. The rankscore is the ratio of the rank of the score over the total number of MTnew scores in dbNSFP. The scores range from 0.0931 to 0.80722
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2c41c1631d1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5
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172 MutationTaster_pred
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6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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173 MutationTaster prediction
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2c41c1631d1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5
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174 MutationTaster_score
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6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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175 MutationTaster p-value (MTori), ranges from 0 to 1
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176 phastCons46way_placental
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177 phastCons conservation score based on the multiple alignments of 33 placental mammal genomes (including human). The larger the score, the more conserved the site
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2c41c1631d1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5
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178 phastCons46way_placental_rankscore
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179 phastCons46way_placental scores were ranked among all phastCons46way_placental scores in dbNSFP. The rankscore is the ratio of the rank of the score over the total number of phastCons46way_placental scores in dbNSFP
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2c41c1631d1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5
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180 phastCons46way_primate
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181 phastCons conservation score based on the multiple alignments of 10 primate genomes (including human). The larger the score, the more conserved the site
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2c41c1631d1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5
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182 phastCons46way_primate_rankscore
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183 phastCons46way_primate scores were ranked among all phastCons46way_primate scores in dbNSFP. The rankscore is the ratio of the rank of the score over the total number of phastCons46way_primate scores in dbNSFP
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2c41c1631d1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5
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184 phastCons100way_vertebrate
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185 phastCons conservation score based on the multiple alignments of 100 vertebrate genomes (including human). The larger the score, the more conserved the site
280
2c41c1631d1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5
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186 phastCons100way_vertebrate_rankscore
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187 phastCons100way_vertebrate scores were ranked among all phastCons100way_vertebrate scores in dbNSFP. The rankscore is the ratio of the rank of the score over the total number of phastCons100way_vertebrate scores in dbNSFP
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188 phyloP46way_placental
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189 phyloP (phylogenetic p-values) conservation score based on the multiple alignments of 33 placental mammal genomes (including human). The larger the score, the more conserved the site
280
2c41c1631d1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5
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190 phyloP46way_placental_rankscore
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6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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191 phyloP46way_placental scores were ranked among all phyloP46way_placental scores in dbNSFP. The rankscore is the ratio of the rank of the score over the total number of phyloP46way_placental scores in dbNSFP
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2c41c1631d1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5
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192 phyloP46way_primate
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iuc
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diff changeset
193 phyloP (phylogenetic p-values) conservation score based on the multiple alignments of 10 primate genomes (including human). The larger the score, the more conserved the site
280
2c41c1631d1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5
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194 phyloP46way_primate_rankscore
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195 phyloP46way_primate scores were ranked among all phyloP46way_primate scores in dbNSFP. The rankscore is the ratio of the rank of the score over the total number of phyloP46way_primate scores in dbNSFP
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2c41c1631d1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5
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196 phyloP100way_vertebrate
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197 phyloP (phylogenetic p-values) conservation score based on the multiple alignments of 100 vertebrate genomes (including human). The larger the score, the more conserved the site
280
2c41c1631d1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5
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198 phyloP100way_vertebrate_rankscore
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199 phyloP100way_vertebrate scores were ranked among all phyloP100way_vertebrate scores in dbNSFP. The rankscore is the ratio of the rank of the score over the total number of phyloP100way_vertebrate scores in dbNSFP
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2c41c1631d1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5
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200 Polyphen2_HDIV_pred
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201 Polyphen2 prediction based on HumDiv
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202 Polyphen2_HDIV_rankscore
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203 Polyphen2 HDIV scores were first ranked among all HDIV scores in dbNSFP. The rankscore is the ratio of the rank the score over the total number of the scores in dbNSFP. If there are multiple scores, only the most damaging (largest) rankscore is presented. The scores range from 0.02656 to 0.89917
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204 Polyphen2_HDIV_score
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205 Polyphen2 score based on HumDiv, i.e. hdiv_prob. The score ranges from 0 to 1. Multiple entries separated by ";"
280
2c41c1631d1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5
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206 Polyphen2_HVAR_pred
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207 Polyphen2 prediction based on HumVar
280
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208 Polyphen2_HVAR_rankscore
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209 Polyphen2 HVAR scores were first ranked among all HVAR scores in dbNSFP. The rankscore is the ratio of the rank the score over the total number of the scores in dbNSFP. If there are multiple scores, only the most damaging (largest) rankscore is presented. The scores range from 0.01281 to 0.9711
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210 Polyphen2_HVAR_score
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6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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211 Polyphen2 score based on HumVar, i.e. hvar_prob. The score ranges from 0 to 1. Multiple entries separated by ";"
280
2c41c1631d1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5
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212 pos(1-coor)
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213 Physical position on the chromosome as to hg19 (1-based coordinate)
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214 RadialSVM_pred
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215 Prediction of our SVM based ensemble prediction score, "T(olerated)" or "D(amaging)". The score cutoff between "D" and "T" is 0. The rankscore cutoff between "D" and "T" is 0.83357
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2c41c1631d1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5
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216 RadialSVM_rankscore
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217 RadialSVM scores were ranked among all RadialSVM scores in dbNSFP. The rankscore is the ratio of the rank of the screo over the total number of RadialSVM scores in dbNSFP. The scores range from 0 to 1
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2c41c1631d1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5
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218 RadialSVM_score
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6c1a0c6cf28c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12a2e9dd273b4c23db48bbb747f32700887710e
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219 Our support vector machine (SVM) based ensemble prediction score, which incorporated 10 scores (SIFT, PolyPhen-2 HDIV, PolyPhen-2 HVAR, GERP++, MutationTaster, Mutation Assessor, FATHMM, LRT, SiPhy, PhyloP) and the maximum frequency observed in the 1000 genomes populations. Larger value means the SNV is more likely to be damaging. Scores range from -2 to 3 in dbNSFP
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220 ref
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221 Reference nucleotide allele (as on the + strand)
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222 refcodon
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223 Reference codon
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224 Reliability_index
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225 Number of observed component scores (except the maximum frequency in the 1000 genomes populations) for RadialSVM and LR. Ranges from 1 to 10. As RadialSVM and LR scores are calculated based on imputed data, the less missing component scores, the higher the reliability of the scores and predictions
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226 SIFT_converted_rankscore
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227 SIFTori scores were first converted to SIFTnew=1-SIFTori, then ranked among all SIFTnew scores in dbNSFP. The rankscore is the ratio of the rank the SIFTnew score over the total number of SIFTnew scores in dbNSFP. If there are multiple scores, only the most damaging (largest) rankscore is presented. The rankscores range from 0.02654 to 0.87932
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228 SIFT_pred
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229 If SIFTori is smaller than 0.05 (rankscore>0.55) the corresponding non-synonymous SNP is predicted as "D(amaging)"; otherwise it is predicted as "T(olerated)". Multiple predictions separated by ";"
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230 SIFT_score
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231 SIFT score (SIFTori). Scores range from 0 to 1. The smaller the score the more likely the SNP has damaging effect. Multiple scores separated by ";"
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232 SiPhy_29way_logOdds
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233 SiPhy score based on 29 mammals genomes. The larger the score, the more conserved the site
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234 SiPhy_29way_pi
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235 The estimated stationary distribution of A, C, G and T at the site, using SiPhy algorithm based on 29 mammals genomes
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236 SLR_test_statistic
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237 SLR test statistic for testing natural selection on codons. A negative value indicates negative selection, and a positive value indicates positive selection. Larger magnitude of the value suggests stronger evidence
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238 Uniprot_aapos
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239 Amino acid position as to Uniprot. Multiple entries separated by ";"
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240 Uniprot_acc
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241 Uniprot accession number. Multiple entries separated by ";"
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242 Uniprot_id
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243 Uniprot ID number. Multiple entries separated by ";"
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244 UniSNP_ids
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245 rs numbers from UniSNP, which is a cleaned version of dbSNP build 129, in format: rs number1;rs number2;...
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246
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247 The dbNSFP database is available from https://sites.google.com/site/jpopgen/dbNSFP and there is only annotation for human genome builds.
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248
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249 The procedure for preparing the dbNSFP data for use in SnpSift dbnsfp and a couple of prebuilt dbNSFP databases are available at:
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250 http://snpeff.sourceforge.net/SnpSift.html#dbNSFP
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251
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252 However, any dbNSFP-like tabular file that be can used with SnpSift dbnsfp if it has:
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253
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254 - The first line of the file must be column headers that name the annotations.
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255 - The first 4 columns are required and must be:
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256
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257 1. chr: chromosome
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258 2. pos(1-coor): position in chromosome
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259 3. ref: reference base
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260 4. alt: alternate base
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261
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262 For example::
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263
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264 #chr pos(1-coor) ref alt aaref aaalt genename SIFT_score
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265 1 69134 A C E A OR4F5 0.03
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266 1 69134 A G E G OR4F5 0.09
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267 1 69134 A T E V OR4F5 0.03
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268 4 100239319 T A H L ADH1B 0
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269 4 100239319 T C H R ADH1B 0.15
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270 4 100239319 T G H P ADH1B 0
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271
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272 The Galaxy datatypes for dbNSFP can automatically convert the specially formatted tabular file for use by SnpSift dbNSFP:
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273
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274 1. Upload the tabular file, set the datatype as: **"dbnsfp.tabular"**
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275 2. Edit the history dataset attributes (pencil icon): Use "Convert Format" to convert the **"dbnsfp.tabular"** to the correct format for SnpSift dbnsfp: **"snpsiftdbnsfp"**.
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277 @EXTERNAL_DOCUMENTATION@
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278 - http://snpeff.sourceforge.net/SnpSift.html#dbNSFP
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279 ]]></help>
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280 <expand macro="citations">
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281 <citation type="doi">10.1002/humu.21517</citation>
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282 <citation type="doi">10.1002/humu.22932</citation>
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283 <citation type="doi">10.1093/hmg/ddu733</citation>
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284 <citation type="doi">10.3389/fgene.2012.00035</citation>
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285 </expand>
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286 </tool>