Mercurial > repos > iuc > snpsift_dbnsfp_generic
diff snpSift_dbnsfp.xml @ 0:0624d484adba draft
Uploaded
| author | iuc |
|---|---|
| date | Thu, 22 Jan 2015 09:08:45 -0500 |
| parents | |
| children | 1f4ee04c0841 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpSift_dbnsfp.xml Thu Jan 22 09:08:45 2015 -0500 @@ -0,0 +1,297 @@ +<tool id="snpSift_dbnsfp_generic" name="SnpSift dbNSFP" version="4.0.0"> + <description>Add Annotations from dbNSFP and similar annotation DBs</description> + <expand macro="requirements" /> + <macros> + <import>snpSift_macros.xml</import> + </macros> + <command> + java -Xmx6G -jar \$SNPEFF_JAR_PATH/SnpSift.jar dbnsfp -v + #if $db.dbsrc == 'cached' : + -db $db.dbnsfp + #if $db.annotations and $db.annotations.__str__ != '': + -f "$db.annotations" + #end if + #else : + -db "${db.dbnsfpdb.extra_files_path}/${db.dbnsfpdb.metadata.bgzip}" + #if $db.annotations and $db.annotations.__str__ != '': + -f "$db.annotations" + #end if + #end if + $input > $output + 2> tmp.err && grep -v file tmp.err + </command> + <inputs> + <param name="input" type="data" format="vcf" label="Variant input file in VCF format"/> + <conditional name="db"> + <param name="dbsrc" type="select" label="dbNSFP "> + <option value="cached">Locally installed dbNSFP database </option> + <option value="history">dbNSFP database from your history</option> + </param> + <when value="cached"> + <param name="dbnsfp" type="select" label="Genome"> + <options from_data_table="snpsift_dbnsfp"> + <column name="name" index="2"/> + <column name="value" index="3"/> + </options> + </param> + <param name="annotations" type="select" multiple="true" display="checkboxes" label="Annotate with"> + <options from_data_table="snpsift_dbnsfp"> + <column name="name" index="3"/> + <column name="value" index="3"/> + <filter type="param_value" ref="dbnsfp" column="2" /> + <filter type="multiple_splitter" column="3" separator=","/> + </options> + </param> + </when> + <when value="history"> + <param name="dbnsfpdb" type="data" format="snpsiftdbnsfp" label="DbNSFP"/> + <param name="annotations" type="select" multiple="true" display="checkboxes" label="Annotate with"> + <options> + <filter type="data_meta" ref="dbnsfpdb" key="annotation" /> + </options> + </param> + </when> + </conditional> + </inputs> + <expand macro="stdio" /> + <outputs> + <data format="vcf" name="output" /> + </outputs> + <tests> + <test> + <param name="input" ftype="vcf" value="test_annotate_in.vcf.vcf"/> + <param name="dbsrc" value="history"/> + <param name="dbnsfpdb" value="test_dbnsfpdb.tabular" ftype="dbnsfp.tabular" /> + <annotations value="aaref,aaalt,genename,aapos,SIFT_score"/> + <output name="output"> + <assert_contents> + <has_text text="dbNSFP_SIFT_score=0.15" /> + </assert_contents> + </output> + </test> + </tests> + <help> + +The dbNSFP is an integrated database of functional predictions from multiple algorithms (SIFT, Polyphen2, LRT and MutationTaster, PhyloP and GERP++, etc.). +It contains variant annotations such as: + + + 1000Gp1_AC + Alternative allele counts in the whole 1000 genomes phase 1 (1000Gp1) data + 1000Gp1_AF + Alternative allele frequency in the whole 1000Gp1 data + 1000Gp1_AFR_AC + Alternative allele counts in the 1000Gp1 African descendent samples + 1000Gp1_AFR_AF + Alternative allele frequency in the 1000Gp1 African descendent samples + 1000Gp1_AMR_AC + Alternative allele counts in the 1000Gp1 American descendent samples + 1000Gp1_AMR_AF + Alternative allele frequency in the 1000Gp1 American descendent samples + 1000Gp1_ASN_AC + Alternative allele counts in the 1000Gp1 Asian descendent samples + 1000Gp1_ASN_AF + Alternative allele frequency in the 1000Gp1 Asian descendent samples + 1000Gp1_EUR_AC + Alternative allele counts in the 1000Gp1 European descendent samples + 1000Gp1_EUR_AF + Alternative allele frequency in the 1000Gp1 European descendent samples + aaalt + Alternative amino acid. "." if the variant is a splicing site SNP (2bp on each end of an intron) + aapos + Amino acid position as to the protein. "-1" if the variant is a splicing site SNP (2bp on each end of an intron) + aapos_SIFT + ENSP id and amino acid positions corresponding to SIFT scores. Multiple entries separated by ";" + aapos_FATHMM + ENSP id and amino acid positions corresponding to FATHMM scores. Multiple entries separated by ";" + aaref + Reference amino acid. "." if the variant is a splicing site SNP (2bp on each end of an intron) + alt + Alternative nucleotide allele (as on the + strand) + Ancestral_allele + Ancestral allele (based on 1000 genomes reference data) + cds_strand + Coding sequence (CDS) strand (+ or -) + chr + Chromosome number + codonpos + Position on the codon (1, 2 or 3) + Ensembl_geneid + Ensembl gene ID + Ensembl_transcriptid + Ensembl transcript IDs (separated by ";") + ESP6500_AA_AF + Alternative allele frequency in the African American samples of the NHLBI GO Exome Sequencing Project (ESP6500 data set) + ESP6500_EA_AF + Alternative allele frequency in the European American samples of the NHLBI GO Exome Sequencing Project (ESP6500 data set) + FATHMM_pred + 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 ";" + FATHMM_rankscore + 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 + FATHMM_score + FATHMM default score (FATHMMori) + fold-degenerate + Degenerate type (0, 2 or 3) + genename + Gene name; if the non-synonymous SNP can be assigned to multiple genes, gene names are separated by ";" + GERP++_NR + GERP++ neutral rate + GERP++_RS + GERP++ RS score, the larger the score, the more conserved the site + GERP++_RS_rankscore + 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 + hg18_pos(1-coor) + Physical position on the chromosome as to hg18 (1-based coordinate) + Interpro_domain + Domain or conserved site on which the variant locates + LR_pred + 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 + LR_rankscore + 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 + LR_score + 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 + LRT_Omega + Estimated nonsynonymous-to-synonymous-rate ratio (Omega, reported by LRT) + LRT_converted_rankscore + 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 + LRT_pred + LRT prediction, D(eleterious), N(eutral) or U(nknown), which is not solely determined by the score + LRT_score + The original LRT two-sided p-value (LRTori), ranges from 0 to 1 + MutationAssessor_pred + MutationAssessor's functional impact of a variant + MutationAssessor_rankscore + 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 + MutationAssessor_score + MutationAssessor functional impact combined score (MAori) + MutationTaster_converted_rankscore + 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 + MutationTaster_pred + MutationTaster prediction + MutationTaster_score + MutationTaster p-value (MTori), ranges from 0 to 1 + phastCons46way_placental + phastCons conservation score based on the multiple alignments of 33 placental mammal genomes (including human). The larger the score, the more conserved the site + phastCons46way_placental_rankscore + 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 + phastCons46way_primate + phastCons conservation score based on the multiple alignments of 10 primate genomes (including human). The larger the score, the more conserved the site + phastCons46way_primate_rankscore + 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 + phastCons100way_vertebrate + phastCons conservation score based on the multiple alignments of 100 vertebrate genomes (including human). The larger the score, the more conserved the site + phastCons100way_vertebrate_rankscore + 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 + phyloP46way_placental + 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 + phyloP46way_placental_rankscore + 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 + phyloP46way_primate + 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 + phyloP46way_primate_rankscore + 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 + phyloP100way_vertebrate + 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 + phyloP100way_vertebrate_rankscore + 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 + Polyphen2_HDIV_pred + Polyphen2 prediction based on HumDiv + Polyphen2_HDIV_rankscore + 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 + Polyphen2_HDIV_score + Polyphen2 score based on HumDiv, i.e. hdiv_prob. The score ranges from 0 to 1. Multiple entries separated by ";" + Polyphen2_HVAR_pred + Polyphen2 prediction based on HumVar + Polyphen2_HVAR_rankscore + 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 + Polyphen2_HVAR_score + Polyphen2 score based on HumVar, i.e. hvar_prob. The score ranges from 0 to 1. Multiple entries separated by ";" + pos(1-coor) + Physical position on the chromosome as to hg19 (1-based coordinate) + RadialSVM_pred + 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 + RadialSVM_rankscore + 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 + RadialSVM_score + 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 + ref + Reference nucleotide allele (as on the + strand) + refcodon + Reference codon + Reliability_index + 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 + SIFT_converted_rankscore + 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 + SIFT_pred + 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 ";" + SIFT_score + 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 ";" + SiPhy_29way_logOdds + SiPhy score based on 29 mammals genomes. The larger the score, the more conserved the site + SiPhy_29way_pi + The estimated stationary distribution of A, C, G and T at the site, using SiPhy algorithm based on 29 mammals genomes + SLR_test_statistic + 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 + Uniprot_aapos + Amino acid position as to Uniprot. Multiple entries separated by ";" + Uniprot_acc + Uniprot accession number. Multiple entries separated by ";" + Uniprot_id + Uniprot ID number. Multiple entries separated by ";" + UniSNP_ids + rs numbers from UniSNP, which is a cleaned version of dbSNP build 129, in format: rs number1;rs number2;... + + + +The procedure for preparing the dbNSFP data for use in SnpSift dbnsfp is in the SnpSift documentation: +http://snpeff.sourceforge.net/SnpSift.html#dbNSFP + +A couple dbNSFP databases are prebuilt for SnpSift at: +http://sourceforge.net/projects/snpeff/files/databases/dbNSFP/ + + + + +**Uploading Your Own Annotations for any Genome** + +The website for dbNSFP databases releases is: +https://sites.google.com/site/jpopgen/dbNSFP + +But there is only annotation for human hg18, hg19, and hg38 genome builds. + +However, any dbNSFP-like tabular file that be can used with SnpSift dbnsfp if it has: + + - The first line of the file must be column headers that name the annotations. + - The first 4 columns are required and must be: + + 1. #chr - chromosome + 2. pos(1-coor) - position in chromosome + 3. ref - reference base + 4. alt - alternate base + + +For example: + +:: + + #chr pos(1-coor) ref alt aaref aaalt genename SIFT_score + 4 100239319 T A H L ADH1B 0 + 4 100239319 T C H R ADH1B 0.15 + 4 100239319 T G H P ADH1B 0 + + +The custom galaxy datatypes for dbNSFP can automatically convert the specially formatted tabular file for use by SnpSift dbNSFP: + 1. Upload the tabular file, set the datatype as: **"dbnsfp.tabular"** + 2. Edit the history dataset attributes (pencil icon): Use "Convert Format" to convert the **"dbnsfp.tabular"** to the correct format for SnpSift dbnsfp: **"snpsiftdbnsfp"**. + +The procedure for preparing the dbNSFP data for use in SnpSift dbnsfp is in the SnpSift documentation. + + +@EXTERNAL_DOCUMENTATION@ + http://snpeff.sourceforge.net/SnpSift.html#dbNSFP + +@CITATION_SECTION@ + + + </help> +</tool>