[2] | 1 | <tool id="hgv_sift" name="SIFT" version="1.0.0"> |
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| 2 | <description>predictions of functional sites</description> |
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| 3 | |
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| 4 | <command interpreter="bash"> |
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| 5 | sift_variants_wrapper.sh "$input" "$output" "${input.metadata.dbkey}" "${GALAXY_DATA_INDEX_DIR}/sift_db.loc" "$chrom_col" "$pos_col" "$base" "$allele_col" "$strand_source.strand_col" "$output_opts" |
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| 6 | </command> |
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| 7 | |
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| 8 | <inputs> |
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| 9 | <param name="input" type="data" format="tabular" label="Dataset"> |
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| 10 | <validator type="unspecified_build"/> |
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| 11 | <validator type="dataset_metadata_in_file" filename="sift_db.loc" metadata_name="dbkey" metadata_column="0" message="Data is currently not available for the specified build."/> |
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| 12 | </param> |
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| 13 | <param name="chrom_col" type="data_column" data_ref="input" label="Column with chromosome"/> |
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| 14 | <param name="pos_col" type="data_column" data_ref="input" numerical="true" label="Column with position"/> |
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| 15 | <param name="base" type="select" label="Position coordinates are"> |
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| 16 | <option value="0">zero-based</option> |
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| 17 | <option value="1" selected="true">one-based</option> |
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| 18 | </param> |
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| 19 | <param name="allele_col" type="data_column" data_ref="input" label="Column with allele"/> |
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| 20 | <conditional name="strand_source"> |
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| 21 | <param name="choice" type="select" label="Strand info"> |
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| 22 | <option value="data_column" selected="true">a column in the dataset</option> |
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| 23 | <option value="all_pos">all on sense/forward/+ strand</option> |
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| 24 | <option value="all_neg">all on antisense/reverse/- strand</option> |
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| 25 | </param> |
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| 26 | <when value="data_column"> |
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| 27 | <param name="strand_col" type="data_column" data_ref="input" label="Column with strand"/> |
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| 28 | </when> |
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| 29 | <when value="all_pos"> |
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| 30 | <param name="strand_col" type="hidden" value="+"/> |
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| 31 | </when> |
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| 32 | <when value="all_neg"> |
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| 33 | <param name="strand_col" type="hidden" value="-"/> |
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| 34 | </when> |
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| 35 | </conditional> |
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| 36 | <param name="output_opts" type="select" multiple="true" display="checkboxes" label="Include the following additional fields in the output"> |
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| 37 | <option value="A">Ensembl Gene ID</option> |
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| 38 | <option value="B">Gene Name</option> |
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| 39 | <option value="C">Gene Description</option> |
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| 40 | <option value="D">Ensembl Protein Family ID</option> |
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| 41 | <option value="E">Ensembl Protein Family Description</option> |
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| 42 | <option value="F">Ensembl Transcript Status (Known / Novel)</option> |
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| 43 | <option value="G">Protein Family Size</option> |
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| 44 | <option value="H">Ka/Ks (Human-mouse)</option> |
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| 45 | <option value="I">Ka/Ks (Human-macaque)</option> |
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| 46 | <option value="J">OMIM Disease</option> |
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| 47 | <option value="K">Allele Frequencies (All Hapmap Populations - weighted average)</option> |
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| 48 | <option value="L">Allele Frequencies (CEU Hapmap population)</option> |
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| 49 | </param> |
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| 50 | </inputs> |
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| 51 | |
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| 52 | <outputs> |
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| 53 | <data format="tabular" name="output" /> |
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| 54 | </outputs> |
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| 55 | |
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| 56 | <requirements> |
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| 57 | <requirement type="binary">awk</requirement> |
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| 58 | <requirement type="binary">rm</requirement> |
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| 59 | <requirement type="binary">sed</requirement> |
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| 60 | </requirements> |
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| 61 | |
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| 62 | <tests> |
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| 63 | <test> |
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| 64 | <param name="input" value="sift_variants.tab" ftype="tabular" dbkey="hg18"/> |
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| 65 | <param name="chrom_col" value="1"/> |
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| 66 | <param name="pos_col" value="3"/> |
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| 67 | <param name="base" value="1"/> |
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| 68 | <param name="allele_col" value="5"/> |
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| 69 | <param name="choice" value="data_column"/> |
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| 70 | <param name="strand_col" value="4"/> |
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| 71 | <param name="output_opts" value="A"/> |
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| 72 | <output name="output" file="sift_variants_result.tab"/> |
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| 73 | </test> |
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| 74 | </tests> |
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| 75 | |
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| 76 | <help> |
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| 77 | .. class:: warningmark |
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| 78 | |
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| 79 | This currently works only for builds hg18 or hg19. |
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| 80 | |
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| 81 | ----- |
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| 82 | |
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| 83 | **Dataset formats** |
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| 84 | |
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| 85 | The input and output datasets are tabular_. |
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| 86 | (`Dataset missing?`_) |
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| 87 | |
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| 88 | .. _tabular: ./static/formatHelp.html#tab |
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| 89 | .. _Dataset missing?: ./static/formatHelp.html |
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| 90 | |
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| 91 | ----- |
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| 92 | |
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| 93 | **What it does** |
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| 94 | |
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| 95 | SIFT predicts whether an amino-acid substitution affects protein function, |
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| 96 | based on sequence homology and the physical properties of amino acids. |
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| 97 | SIFT can be applied to naturally occurring non-synonymous polymorphisms |
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| 98 | and laboratory-induced missense mutations. This tool uses SQLite databases |
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| 99 | containing pre-computed SIFT scores and annotations for all possible nucleotide |
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| 100 | substitutions at each position in the human exome. Allele frequency data |
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| 101 | are from the HapMap frequency database, and additional transcript and |
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| 102 | gene-level data are from Ensembl BioMart. |
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| 103 | |
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| 104 | The input dataset must contain columns for the chromosome, position, and |
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| 105 | alleles. The alleles must be two nucleotides separated by '/', |
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| 106 | usually the reference allele and the allele of interest. |
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| 107 | The strand must either be in another column or all the same. |
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| 108 | The output contains a standard set of columns plus the additional ones that |
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| 109 | have been selected from the list above. |
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| 110 | |
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| 111 | Website: http://sift.jcvi.org/ |
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| 112 | |
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| 113 | ----- |
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| 114 | |
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| 115 | **Example** |
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| 116 | |
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| 117 | - input file:: |
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| 118 | |
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| 119 | chr3 81780820 + T/C |
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| 120 | chr2 230341630 + G/A |
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| 121 | chr2 43881517 + A/T |
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| 122 | chr2 43857514 + T/C |
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| 123 | chr6 88375602 + G/A |
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| 124 | chr22 29307353 - T/A |
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| 125 | chr10 115912482 - G/T |
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| 126 | chr10 115900918 - C/T |
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| 127 | chr16 69875502 + G/T |
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| 128 | etc. |
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| 129 | |
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| 130 | - output file:: |
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| 131 | |
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| 132 | #Chrom Position Strand Allele Codons Transcript ID Protein ID Substitution Region dbSNP ID SNP Type Prediction Score Median Info Num seqs at position User Comment |
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| 133 | chr3 81780820 + T/C AGA-gGA ENST00000264326 ENSP00000264326 R190G EXON CDS rs2229519:C Nonsynonymous DAMAGING 0.04 3.06 149 |
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| 134 | chr2 230341630 + G/T - ENST00000389045 ENSP00000373697 NA EXON CDS rs1803846:A Unknown Not scored NA NA NA |
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| 135 | chr2 43881517 + A/T ATA-tTA ENST00000260605 ENSP00000260605 I230L EXON CDS rs11556157:T Nonsynonymous TOLERATED 0.47 3.19 7 |
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| 136 | chr2 43857514 + T/C TTT-TcT ENST00000260605 ENSP00000260605 F33S EXON CDS rs2288709:C Nonsynonymous TOLERATED 0.61 3.33 6 |
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| 137 | chr6 88375602 + G/A GTT-aTT ENST00000257789 ENSP00000257789 V217I EXON CDS rs2307389:A Nonsynonymous TOLERATED 0.75 3.17 13 |
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| 138 | chr22 29307353 + T/A ACC-tCC ENST00000335214 ENSP00000334612 T264S EXON CDS rs42942:A Nonsynonymous TOLERATED 0.4 3.14 23 |
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| 139 | chr10 115912482 + C/A CGA-CtA ENST00000369285 ENSP00000358291 R179L EXON CDS rs12782946:T Nonsynonymous TOLERATED 0.06 4.32 2 |
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| 140 | chr10 115900918 + G/A CAA-tAA ENST00000369287 ENSP00000358293 Q271* EXON CDS rs7095762:T Nonsynonymous N/A N/A N/A N/A |
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| 141 | chr16 69875502 + G/T ACA-AaA ENST00000338099 ENSP00000337512 T608K EXON CDS rs3096381:T Nonsynonymous TOLERATED 0.12 3.41 3 |
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| 142 | etc. |
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| 143 | |
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| 144 | ----- |
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| 145 | |
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| 146 | **References** |
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| 147 | |
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| 148 | Ng PC, Henikoff S. (2001) Predicting deleterious amino acid substitutions. |
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| 149 | Genome Res. 11(5):863-74. |
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| 150 | |
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| 151 | Ng PC, Henikoff S. (2002) Accounting for human polymorphisms predicted to affect protein function. |
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| 152 | Genome Res. 12(3):436-46. |
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| 153 | |
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| 154 | Ng PC, Henikoff S. (2003) SIFT: Predicting amino acid changes that affect protein function. |
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| 155 | Nucleic Acids Res. 31(13):3812-4. |
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| 156 | |
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| 157 | Kumar P, Henikoff S, Ng PC. (2009) Predicting the effects of coding non-synonymous variants |
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| 158 | on protein function using the SIFT algorithm. |
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| 159 | Nat Protoc. 4(7):1073-81. Epub 2009 Jun 25. |
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| 160 | |
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| 161 | </help> |
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| 162 | </tool> |
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