| Next changeset 1:13191d4914f7 (2016-06-07) |
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readme.rst repository_dependencies.xml snpSift_dbnsfp.xml snpSift_macros.xml test-data/test_annotate_in.vcf test-data/test_dbnsfp_out.vcf test-data/test_dbnsfpdb.tabular tool-data/snpsift_dbnsfp.loc.sample tool_data_table_conf.xml.sample tool_dependencies.xml |
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| diff -r 000000000000 -r dc480609d9c1 readme.rst --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/readme.rst Thu Jan 22 08:53:21 2015 -0500 |
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| @@ -0,0 +1,11 @@ +These are galaxy tools for SnpEff a variant annotation and effect prediction tool by Pablo Cingolani. +It annotates and predicts the effects of variants on genes (such as amino acid changes). +( http://snpeff.sourceforge.net/ ) + +This repository contains a tool_dependencies.xml file that will attempt to automatically install SnpEff and SnpSift. + +SnpEff citation: +"A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3.", Cingolani P, Platts A, Wang le L, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM. Fly (Austin). 2012 Apr-Jun;6(2):80-92. PMID: 22728672 [PubMed - in process] + +SnpSift citation: +"Using Drosophila melanogaster as a model for genotoxic chemical mutational studies with a new program, SnpSift", Cingolani, P., et. al., Frontiers in Genetics, 3, 2012. |
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| diff -r 000000000000 -r dc480609d9c1 repository_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/repository_dependencies.xml Thu Jan 22 08:53:21 2015 -0500 |
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| @@ -0,0 +1,4 @@ +<?xml version="1.0"?> +<repositories description="This requires the SnpEff dbnsfp datatype definitions."> + <repository changeset_revision="0c4372b93e85" name="snpsift_dbnsfp_datatypes" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> +</repositories> |
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| diff -r 000000000000 -r dc480609d9c1 snpSift_dbnsfp.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpSift_dbnsfp.xml Thu Jan 22 08:53:21 2015 -0500 |
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| b'@@ -0,0 +1,281 @@\n+<tool id="snpSift_dbnsfp" name="SnpSift dbNSFP" version="4.0.0">\n+ <description>Add Annotations from dbNSFP</description>\n+ <expand macro="requirements" />\n+ <macros>\n+ <import>snpSift_macros.xml</import>\n+ </macros>\n+ <command>\n+ java -Xmx6G -jar \\$SNPEFF_JAR_PATH/SnpSift.jar dbnsfp -v\n+ #if $db.dbsrc == \'cached\' :\n+ -db $db.dbnsfp \n+ #if $db.annotations and $db.annotations.__str__ != \'\':\n+ -f "$db.annotations"\n+ #end if\n+ #else :\n+ -db "${db.dbnsfpdb.extra_files_path}/${db.dbnsfpdb.metadata.bgzip}"\n+ #if $db.annotations and $db.annotations.__str__ != \'\':\n+ -f "$db.annotations"\n+ #end if\n+ #end if \n+ $input > $output \n+ 2> tmp.err && grep -v file tmp.err\n+ </command>\n+ <inputs>\n+ <param name="input" type="data" format="vcf" label="Variant input file in VCF format"/>\n+ <conditional name="db">\n+ <param name="dbsrc" type="select" label="dbNSFP ">\n+ <option value="cached">Locally installed dbNSFP database </option>\n+ <option value="history">dbNSFP database from your history</option>\n+ </param>\n+ <when value="cached">\n+ <param name="dbnsfp" type="select" label="Genome">\n+ <options from_data_table="snpsift_dbnsfp">\n+ <column name="name" index="1"/>\n+ <column name="value" index="2"/>\n+ </options>\n+ </param>\n+ <param name="annotations" type="select" multiple="true" display="checkboxes" label="Annotate with">\n+ <options from_data_table="snpsift_dbnsfp">\n+ <column name="name" index="3"/>\n+ <column name="value" index="3"/>\n+ <filter type="param_value" ref="dbnsfp" column="2" />\n+ <filter type="multiple_splitter" column="3" separator=","/>\n+ </options>\n+ </param>\n+ </when>\n+ <when value="history">\n+ <param name="dbnsfpdb" type="data" format="snpsiftdbnsfp" label="DbNSFP"/>\n+ <param name="annotations" type="select" multiple="true" display="checkboxes" label="Annotate with">\n+ <options>\n+ <filter type="data_meta" ref="dbnsfpdb" key="annotation" />\n+ </options>\n+ </param>\n+ </when>\n+ </conditional>\n+ </inputs>\n+ <expand macro="stdio" />\n+ <outputs>\n+ <data format="vcf" name="output" />\n+ </outputs>\n+ <tests>\n+ <test>\n+ <param name="input" ftype="vcf" value="test_annotate_in.vcf.vcf"/>\n+ <param name="dbsrc" value="history"/>\n+ <param name="dbnsfpdb" value="test_dbnsfpdb.tabular" ftype="dbnsfp.tabular" />\n+ <annotations value="aaref,aaalt,genename,aapos,SIFT_score"/>\n+ <output name="output">\n+ <assert_contents>\n+ <has_text text="dbNSFP_SIFT_score=0.15" />\n+ </assert_contents>\n+ </output>\n+ </test>\n+ </tests>\n+ <help>\n+\n+The dbNSFP is an integrated database of functional predictions from multiple algorithms (SIFT, Polyphen2, LRT and MutationTaster, PhyloP and GERP++, etc.).\n+\n+\n+ 1000Gp1_AC\n+ Alternative allele counts in the whole 1000 genomes phase 1 (1000Gp1) data\n+ 1000Gp1_AF\n+ Alternative allele frequency in the whole 1000Gp1 data\n+ 1000Gp1_AFR_AC\n+ Alternative allele counts in the 1000Gp1 African descendent samples\n+ 1000Gp1_AFR_AF\n+ Alternative allele frequency in the 1000Gp1 African descendent samples\n+ 1000Gp1_AMR_AC\n+ Alternative allele counts in the 1000Gp1 American descendent samples\n+ 1000Gp1_AMR_AF\n+ Alternative allele frequency in the 1000Gp1 American descendent samples\n+ 1000Gp1_ASN_AC\n+ '..b'n 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\n+ RadialSVM_rankscore\n+ 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\n+ RadialSVM_score\n+ 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\n+ ref\n+ Reference nucleotide allele (as on the + strand)\n+ refcodon\n+ Reference codon\n+ Reliability_index\n+ 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\n+ SIFT_converted_rankscore\n+ 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\n+ SIFT_pred\n+ 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 ";"\n+ SIFT_score\n+ 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 ";"\n+ SiPhy_29way_logOdds\n+ SiPhy score based on 29 mammals genomes. The larger the score, the more conserved the site\n+ SiPhy_29way_pi\n+ The estimated stationary distribution of A, C, G and T at the site, using SiPhy algorithm based on 29 mammals genomes\n+ SLR_test_statistic\n+ 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\n+ Uniprot_aapos\n+ Amino acid position as to Uniprot. Multiple entries separated by ";"\n+ Uniprot_acc\n+ Uniprot accession number. Multiple entries separated by ";"\n+ Uniprot_id\n+ Uniprot ID number. Multiple entries separated by ";"\n+ UniSNP_ids\n+ rs numbers from UniSNP, which is a cleaned version of dbSNP build 129, in format: rs number1;rs number2;...\n+\n+\n+The website for dbNSFP database is https://sites.google.com/site/jpopgen/dbNSFP and there is only annotation for human hg18 and hg19 genome builds. \n+\n+However, any dbNSFP-like tabular file that be can used with SnpSift dbnsfp if it has::\n+\n+\t- The first line of the file must be column headers that name the annotations. \n+\t- The first 4 columns are required and must be::\n+\t\t1. chromosome \n+\t\t2. position in chromosome\n+\t\t3. reference base\n+\t\t4. alternate base\n+\n+For example:\n+\n+::\n+\n+\t#chr\tpos(1-coor)\tref\talt\taaref\taaalt\tgenename\tSIFT_score\n+\t1\t69134\tA\tC\tE\tA\tOR4F5\t0.03\n+\t1\t69134\tA\tG\tE\tG\tOR4F5\t0.09\n+\t1\t69134\tA\tT\tE\tV\tOR4F5\t0.03\n+\t4\t100239319\tT\tA\tH\tL\tADH1B\t0\n+\t4\t100239319\tT\tC\tH\tR\tADH1B\t0.15\n+\t4\t100239319\tT\tG\tH\tP\tADH1B\t0\n+\n+\n+The uploaded tabular file should be set to datatype: "dbnsfp.tabular"\n+Using "Convert Format" the "dbnsfp.tabular" can be converted to the correct format for SnpSift dbnsfp.\n+\n+The procedure for preparing the dbNSFP data for use in SnpSift dbnsfp is in the SnpSift documentation.\n+\n+\n+@EXTERNAL_DOCUMENTATION@\n+\thttp://snpeff.sourceforge.net/SnpSift.html#dbNSFP\n+\n+@CITATION_SECTION@\n+\n+\n+ </help>\n+</tool>\n' |
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| diff -r 000000000000 -r dc480609d9c1 snpSift_macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpSift_macros.xml Thu Jan 22 08:53:21 2015 -0500 |
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| @@ -0,0 +1,35 @@ +<macros> + <xml name="requirements"> + <requirements> + <requirement type="package" version="4.0">snpEff</requirement> + </requirements> + </xml> + <xml name="stdio"> + <stdio> + <exit_code range=":-1" level="fatal" description="Error: Cannot open file" /> + <exit_code range="1:" level="fatal" description="Error" /> + </stdio> + </xml> + <token name="@EXTERNAL_DOCUMENTATION@"> + +For details about this tool, please go to: + http://snpeff.sourceforge.net/SnpEff_manual.html + + </token> + <token name="@CITATION_SECTION@">------ + +**Citation** + +For the underlying tool, please cite the following two publications: + +SnpSift citation: +"Using Drosophila melanogaster as a model for genotoxic chemical mutational studies with a new program, SnpSift", Cingolani, P., et. al., Frontiers in Genetics, 3:35, 2012. + + </token> + <xml name="citations"> + <citations> + <citation type="doi">10.3389/fgene.2012.00035</citation> + <yield /> + </citations> + </xml> +</macros> |
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| diff -r 000000000000 -r dc480609d9c1 test-data/test_annotate_in.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_annotate_in.vcf Thu Jan 22 08:53:21 2015 -0500 |
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| @@ -0,0 +1,10 @@ +##fileformat=VCFv4.1 +##samtoolsVersion=0.1.18 (r982:295) +##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth"> +##SnpEffVersion="3.5 (build 2014-02-12), by Pablo Cingolani" +##SnpEffCmd="SnpEff -i vcf -o vcf -upDownStreamLen 5000 -spliceSiteSize 1 -stats /Users/jj/gxt/gxt/database/files/004/dataset_4998.dat GRCh37.71 /Users/jj/gxt/gxt/database/files/004/dataset_4996.dat " +##INFO=<ID=EFF,Number=.,Type=String,Description="Predicted effects for this variant.Format: 'Effect ( Effect_Impact | Functional_Class | Codon_Change | Amino_Acid_Change| Amino_Acid_length | Gene_Name | Transcript_BioType | Gene_Coding | Transcript_ID | Exon_Rank | Genotype_Number [ | ERRORS | WARNINGS ] )' "> +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT /data/sequencing/output/biotec4/mapping/L774.q1.s.bam /data/sequencing/output/biotec4/mapping/L775.q1.s.bam +chr4 100239319 rs1229984 T C 94.3 . DP=29;EFF=EXON(MODIFIER|||||ADH1B|processed_transcript|CODING|ENST00000504498|3|1),EXON(MODIFIER|||||ADH1B|retained_intron|CODING|ENST00000515694|3|1),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAc/cGc|H48R|375|ADH1B|protein_coding|CODING|ENST00000305046|3|1),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAc/cGc|H8R|335|ADH1B|protein_coding|CODING|ENST00000394887|3|1),UTR_3_PRIME(MODIFIER||2729|||ADH1B|nonsense_mediated_decay|CODING|ENST00000506651|4|1) +chr12 32491626 rs1471909 G A 124.0 . DP=22;EFF=DOWNSTREAM(MODIFIER||532|||BICD1|retained_intron|CODING|ENST00000552160||1),INTRON(MODIFIER||||835|BICD1|protein_coding|CODING|ENST00000548411|7|1),INTRON(MODIFIER||||975|BICD1|protein_coding|CODING|ENST00000281474|7|1),INTRON(MODIFIER|||||BICD1|nonsense_mediated_decay|CODING|ENST00000395758|7|1),INTRON(MODIFIER|||||BICD1|retained_intron|CODING|ENST00000552226|1|1) +chrX 153010066 rs11803 C T 73.8 . DP=34;EFF=DOWNSTREAM(MODIFIER||4008||221|ABCD1|protein_coding|CODING|ENST00000443684||1),INTRAGENIC(MODIFIER|||||ABCD1||CODING|||1),INTRON(MODIFIER|||||U52111.14|antisense|NON_CODING|ENST00000434284|1|1),UTR_3_PRIME(MODIFIER||877||745|ABCD1|protein_coding|CODING|ENST00000218104|10|1) |
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| diff -r 000000000000 -r dc480609d9c1 test-data/test_dbnsfp_out.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_dbnsfp_out.vcf Thu Jan 22 08:53:21 2015 -0500 |
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| @@ -0,0 +1,15 @@ +##fileformat=VCFv4.1 +##samtoolsVersion=0.1.18 (r982:295) +##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth"> +##SnpEffVersion="3.5 (build 2014-02-12), by Pablo Cingolani" +##SnpEffCmd="SnpEff -i vcf -o vcf -upDownStreamLen 5000 -spliceSiteSize 1 -stats /Users/jj/gxt/gxt/database/files/004/dataset_4998.dat GRCh37.71 /Users/jj/gxt/gxt/database/files/004/dataset_4996.dat " +##INFO=<ID=EFF,Number=.,Type=String,Description="Predicted effects for this variant.Format: 'Effect ( Effect_Impact | Functional_Class | Codon_Change | Amino_Acid_Change| Amino_Acid_length | Gene_Name | Transcript_BioType | Gene_Coding | Transcript_ID | Exon_Rank | Genotype_Number [ | ERRORS | WARNINGS ] )' "> +##SnpSiftVersion="SnpSift 3.5 (build 2014-02-12), by Pablo Cingolani" +##SnpSiftCmd="SnpSift dbnsfp /Users/jj/gxt/gxt/database/files/005/dataset_5011_files/dbNSFP.gz -f aaref,aaalt,genename,aapos,SIFT_score /Users/jj/gxt/gxt/database/files/005/dataset_5006.dat " +##INFO=<ID=dbNSFP_aapos,Number=A,Type=Integer,Description="Field 'aapos' from dbNSFP"> +##INFO=<ID=dbNSFP_genename,Number=A,Type=String,Description="Field 'genename' from dbNSFP"> +##INFO=<ID=dbNSFP_aaref,Number=A,Type=Character,Description="Field 'aaref' from dbNSFP"> +##INFO=<ID=dbNSFP_aaalt,Number=A,Type=Character,Description="Field 'aaalt' from dbNSFP"> +##INFO=<ID=dbNSFP_SIFT_score,Number=A,Type=Float,Description="Field 'SIFT_score' from dbNSFP"> +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT /data/sequencing/output/biotec4/mapping/L774.q1.s.bam /data/sequencing/output/biotec4/mapping/L775.q1.s.bam +chr4 100239319 rs1229984 T C 94.3 . DP=29;EFF=EXON(MODIFIER|||||ADH1B|processed_transcript|CODING|ENST00000504498|3|1),EXON(MODIFIER|||||ADH1B|retained_intron|CODING|ENST00000515694|3|1),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAc/cGc|H48R|375|ADH1B|protein_coding|CODING|ENST00000305046|3|1),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAc/cGc|H8R|335|ADH1B|protein_coding|CODING|ENST00000394887|3|1),UTR_3_PRIME(MODIFIER||2729|||ADH1B|nonsense_mediated_decay|CODING|ENST00000506651|4|1);dbNSFP_aapos=48|8|48;dbNSFP_genename=ADH1B;dbNSFP_aaref=H;dbNSFP_aaalt=R;dbNSFP_SIFT_score=0.15 |
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| diff -r 000000000000 -r dc480609d9c1 test-data/test_dbnsfpdb.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_dbnsfpdb.tabular Thu Jan 22 08:53:21 2015 -0500 |
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| @@ -0,0 +1,7 @@ +#chr pos(1-coor) ref alt aaref aaalt hg18_pos(1-coor) genename Uniprot_acc Uniprot_id Uniprot_aapos Interpro_domain cds_strand refcodon SLR_test_statistic codonpos fold-degenerate Ancestral_allele Ensembl_geneid Ensembl_transcriptid aapos aapos_SIFT aapos_FATHMM SIFT_score SIFT_converted_rankscore SIFT_pred Polyphen2_HDIV_score Polyphen2_HDIV_rankscore Polyphen2_HDIV_pred Polyphen2_HVAR_score Polyphen2_HVAR_rankscore Polyphen2_HVAR_pred LRT_score LRT_converted_rankscore LRT_pred MutationTaster_score MutationTaster_converted_rankscore MutationTaster_pred MutationAssessor_score MutationAssessor_rankscore MutationAssessor_pred FATHMM_score FATHMM_rankscore FATHMM_pred RadialSVM_score RadialSVM_rankscore RadialSVM_pred LR_score LR_rankscore LR_pred Reliability_index CADD_raw CADD_raw_rankscore CADD_phred GERP++_NR GERP++_RS GERP++_RS_rankscore phyloP46way_primate phyloP46way_primate_rankscore phyloP46way_placental phyloP46way_placental_rankscore phyloP100way_vertebrate phyloP100way_vertebrate_rankscore phastCons46way_primate phastCons46way_primate_rankscore phastCons46way_placental phastCons46way_placental_rankscore phastCons100way_vertebrate phastCons100way_vertebrate_rankscore SiPhy_29way_pi SiPhy_29way_logOdds SiPhy_29way_logOdds_rankscore LRT_Omega UniSNP_ids 1000Gp1_AC 1000Gp1_AF 1000Gp1_AFR_AC 1000Gp1_AFR_AF 1000Gp1_EUR_AC 1000Gp1_EUR_AF 1000Gp1_AMR_AC 1000Gp1_AMR_AF 1000Gp1_ASN_AC 1000Gp1_ASN_AF ESP6500_AA_AF ESP6500_EA_AF +1 69134 A C E A 58997 OR4F5 Q8NH21 OR4F5_HUMAN 15 . + GAA . 2 0 . ENSG00000186092 ENST00000534990;ENST00000335137 63;15 ENSP00000334393:E15A ENSP00000334393:E15A 0.03 0.62326 D 0.043 0.20261 B 0.037 0.21917 B 0.263780 0.15411 U 0.998654 0.22851 N 2.635 0.83312 M 7.42 0.00438 T -0.9897 0.32693 T 0.0017 0.00524 T 10 -0.186758 0.06340 3.092 2.31 2.31 0.28768 0.327000 0.21459 1.014000 0.39417 0.296000 0.19083 0.475000 0.33008 0.951000 0.38953 0.000000 0.05858 1.0:0.0:0.0:0.0 8.5094 0.33208 0.481469 . . . . . . . . . . . . . +1 69134 A G E G 58997 OR4F5 Q8NH21 OR4F5_HUMAN 15 . + GAA . 2 0 . ENSG00000186092 ENST00000534990;ENST00000335137 63;15 ENSP00000334393:E15G ENSP00000334393:E15G 0.09 0.49607 T 0.0 0.02656 B 0.001 0.04013 B 0.263780 0.15411 N 0.998383 0.23043 N 2.055 0.67517 M 7.4 0.00444 T -0.9720 0.37103 T 0.0013 0.00412 T 10 -0.469020 0.04445 1.834 2.31 2.31 0.28768 0.327000 0.21459 1.014000 0.39417 0.296000 0.19083 0.475000 0.33008 0.951000 0.38953 0.000000 0.05858 1.0:0.0:0.0:0.0 8.5094 0.33208 0.481469 . . . . . . . . . . . . . +1 69134 A T E V 58997 OR4F5 Q8NH21 OR4F5_HUMAN 15 . + GAA . 2 0 . ENSG00000186092 ENST00000534990;ENST00000335137 63;15 ENSP00000334393:E15V ENSP00000334393:E15V 0.03 0.62326 D 0.308 0.31100 B 0.18 0.34346 B 0.263780 0.15411 U 0.996706 0.23838 N 2.57 0.82056 M 7.39 0.00446 T -1.0029 0.28902 T 0.0017 0.00524 T 10 0.661265 0.14645 7.544 2.31 2.31 0.28768 0.327000 0.21459 1.014000 0.39417 0.296000 0.19083 0.475000 0.33008 0.951000 0.38953 0.000000 0.05858 1.0:0.0:0.0:0.0 8.5094 0.33208 0.481469 . . . . . . . . . . . . . +4 100239319 T A H L 100458342 ADH1B A8MYN5 . 8 . - CAC -1.2513 2 0 C ENSG00000196616 ENST00000305046;ENST00000394887;ENST00000412614 48;8;48 ENSP00000306606:H48L ENSP00000306606:H48L;ENSP00000378351:H8L 0 0.87932 D 0.021 0.17268 B 0.009 0.13407 B 0.001009 0.40818 N 0.962682 0.39176 D 1.11 0.37507 L 3.73;3.49 0.05139 T;T -1.0300 0.19614 T 0.0167 0.06508 T 10 2.521929 0.44866 14.39 4.41 3.57 0.40892 -0.215000 0.12644 0.318000 0.23185 2.012000 0.40932 0.849000 0.48306 0.053000 0.19242 0.997000 0.39634 0.0:0.8397:0.0:0.1603 10.5345 0.44996 0.280785 . . . . . . . . . . . . . +4 100239319 T C H R 100458342 ADH1B A8MYN5 . 8 . - CAC -1.2513 2 0 C ENSG00000196616 ENST00000305046;ENST00000394887;ENST00000412614 48;8;48 ENSP00000306606:H48R ENSP00000306606:H48R;ENSP00000378351:H8R 0.15 0.41790 T 0.0 0.02656 B 0.0 0.01281 B 0.001009 0.40818 N 0.848429 0.29591 P . . . 3.8;3.52 0.04970 T;T -0.9979 0.30416 T 0.0000 0.00012 T 8 0.445290 0.12164 6.418 4.41 3.57 0.40892 -0.215000 0.12644 0.318000 0.23185 2.012000 0.40932 0.849000 0.48306 0.053000 0.19242 0.997000 0.39634 0.0:0.8397:0.0:0.1603 10.5345 0.44996 0.280785 rs1229984;rs1789884;rs11537716;rs17028836;rs17856968;rs52797169;rs57624638;rs1229984 1723 0.7889194139194139 492 1.0 744 0.9815303430079155 332 0.9171270718232044 155 0.270979020979021 0.983886 0.953023 +4 100239319 T G H P 100458342 ADH1B A8MYN5 . 8 . - CAC -1.2513 2 0 C ENSG00000196616 ENST00000305046;ENST00000394887;ENST00000412614 48;8;48 ENSP00000306606:H48P ENSP00000306606:H48P;ENSP00000378351:H8P 0 0.87932 D 0.0 0.02656 B 0.002 0.06405 B 0.001009 0.40818 N 0.961891 0.39133 D 0.42 0.16602 N 3.72;3.47 0.05258 T;T -0.9816 0.34750 T 0.0130 0.04815 T 10 2.210304 0.39003 13.35 4.41 3.57 0.40892 -0.215000 0.12644 0.318000 0.23185 2.012000 0.40932 0.849000 0.48306 0.053000 0.19242 0.997000 0.39634 0.0:0.8397:0.0:0.1603 10.5345 0.44996 0.280785 . . . . . . . . . . . . . |
| b |
| diff -r 000000000000 -r dc480609d9c1 tool-data/snpsift_dbnsfp.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/snpsift_dbnsfp.loc.sample Thu Jan 22 08:53:21 2015 -0500 |
| b |
| @@ -0,0 +1,2 @@ +#id desc path annotations +#GRCh37_dbNSFP2.1 GRCh37 dbNSFP2.1 /depot/snpeff/ SIFT_pred,Uniprot_acc |
| b |
| diff -r 000000000000 -r dc480609d9c1 tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Thu Jan 22 08:53:21 2015 -0500 |
| b |
| @@ -0,0 +1,7 @@ +<tables> + <table name="snpsift_dbnsfp" comment_char="#"> + <columns>dbkey, name, value, annotations</columns> + <file path="tool-data/snpsift_dbnsfp.loc" /> + </table> +</tables> + |
| b |
| diff -r 000000000000 -r dc480609d9c1 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Thu Jan 22 08:53:21 2015 -0500 |
| b |
| @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="snpEff" version="4.0"> + <repository changeset_revision="6bc55957927b" name="package_snpeff_4_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency> |