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Migrated tool version 0.9 from old tool shed archive to new tool shed repository
author pcingola
date Tue, 07 Jun 2011 17:08:59 -0400
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1 <tool id="snpEff" name="Compute SNP effect" version="0.9">
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2 <description>for each SNP in a file</description>
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3 <command>java -jar /usr/local/snpEff/snpEff.jar -c /usr/local/snpEff/snpEff.config $genomeVersion $input > $output</command>
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4 <!-- <command>java -Xmx2048M -jar /usr/local/snpEff/snpEff.jar -c /usr/local/snpEff/snpEff.config $genomeVersion $input > $output</command> -->
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5 <inputs>
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6 <param format="interval" name="input" type="data" label="Source file"/>
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7 <param name="genomeVersion" type="select" label="Genome">
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8 <option value="hg37">Human (hg37)</option>
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9 <option value="mm37">Mouse (mm37)</option>
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10 </param>
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11 </inputs>
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12 <outputs>
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13 <data format="tabular" name="output" />
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14 </outputs>
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15
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16 <help>
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17
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18 This tool computes the effect of SNPs. Current predictions include
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19
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20 * GENE : ENSEMBL gene ID, gene name and bio-type
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21 * TRANSCRIPT : ENSEMBL transcript ID
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22 * INTRON : The SNP hits a transcript, but no exons (or UTRs)
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23 * EXON : ENSEMBL exon ID
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24 * SYNONYMOUS_CODING : The SNP changes the DNA sequence in a way that produces the same amino acid
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25 * NON_SYNONYMOUS_CODING : The SNP changes the DNA sequence in a way that produces a different amino acid
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26 * STOP_GAINED : The SNP creates a new STOP codon
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27 * STOP_LOST : The SNP changes a STOP codon into an amino acid
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28 * UPSTREAM : The SNP is 2K bases upstream of a transcript (before 5 prime UTR)
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29 * DOWNSTREAM : The SNP is 2K bases downstream of a transcript (after 3 prime UTR)
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30 * 5PRIME_UTR : The SNP is in the 5 prime UTR region
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31 * 3PRIME_UTR : The SNP is in the 3 prime UTR region
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32 * INTERGENIC : The SNP does not any known gene or up/downstream region
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33
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34 -----
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35
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36 .. class:: infomark
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37
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38 **File format**
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39
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40 The file format must be tab-separated format, containing five columns that correspond to:
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41
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42 * chromosome_name
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43 * chromosome_start_position
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44 * chromosome_end_position
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45 * allele: "base_Ori / base_Snp"
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46 * strand: {+,-}
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47
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48 .. class:: warningmark
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49
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50 **WARNING** Insertions and deletions are not supported, so chromosome_start_position is equal to chromosome_end_position::
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51
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52 -----
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53
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54 .. class:: infomark
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55
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56 **Input file format example**
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57
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58 This is an example of an input file::
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59
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60 5 140532 140532 T/C +
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61 12 1017956 1017956 T/A +
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62 2 946507 946507 G/C +
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63 14 19584687 19584687 C/T -
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64 19 66520 66520 G/A +
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65 8 150029 150029 A/T +
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66
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67 -----
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68
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69 .. class:: infomark
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70
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71 **Output file format example**
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72
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73 The output file consist of one line per SNP effect. This means that you usually get more than one line per SNP. The format is tab separated cinsisting of two columns
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74
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75 * SNP: chr:position_besOri/baseSnp
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76 * Effect : Effect[, EXON:ExonId, TRANSCRIPT:TranscriptId, GENE:GeneId (genenName bioType)]
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77
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78 This is an example of an output file::
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79
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80 chr2:946507_G/C UPSTREAM, ENST00000452177
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81 chr2:946507_G/C UPSTREAM, ENST00000450962
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82 chr2:946507_G/C UPSTREAM, ENST00000308624
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83 chr2:946507_G/C UPSTREAM, ENST00000407292
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84 chr5:140532_T/C NON_SYNONYMOUS_CODING (V/A), EXON:ENSE00001319336, TRANSCRIPT:ENST00000283426, GENE:ENSG00000153404(PLEKHG4B protein_coding)
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85 chr5:140532_T/C NON_SYNONYMOUS_CODING (V/A), EXON:ENSE00001319336, TRANSCRIPT:ENST00000398036, GENE:ENSG00000153404(PLEKHG4B protein_coding)
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86 chr5:140532_T/C DOWNSTREAM, ENST00000398036
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87 chr8:150029_A/T NON_SYNONYMOUS_CODING (Y/N), EXON:ENSE00001913609, TRANSCRIPT:ENST00000490482, GENE:ENSG00000223508(RPL23AP53 protein_coding)
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88 chr12:1017956_T/A STOP_LOST (*/K), EXON:ENSE00001527897, TRANSCRIPT:ENST00000340908, GENE:ENSG00000060237(WNK1 protein_coding)
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89 chr12:1017956_T/A STOP_LOST (*/K), EXON:ENSE00001527897, TRANSCRIPT:ENST00000252477, GENE:ENSG00000060237(WNK1 protein_coding)
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90 chr12:1017956_T/A STOP_LOST (*/K), EXON:ENSE00001527897, TRANSCRIPT:ENST00000315939, GENE:ENSG00000060237(WNK1 protein_coding)
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91 chr12:1017956_T/A UPSTREAM, ENST00000340908
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92 chr14:19584687_C/T 3PRIME_UTR, ENSE00001583193, TRANSCRIPT:ENST00000409832, GENE:ENSG00000222036(POTEG protein_coding)
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93
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94 .. class:: warningmark
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95
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96 **WARNING** You may get the same effect on one exon repeated because it acts on different transcripts::
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97 </help>
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98 </tool>
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99