# HG changeset patch
# User iuc
# Date 1421935725 18000
# Node ID 0624d484adbaf726ebb0a410dfecc22009b622da
Uploaded
diff -r 000000000000 -r 0624d484adba readme.rst
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/readme.rst Thu Jan 22 09:08:45 2015 -0500
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+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.
diff -r 000000000000 -r 0624d484adba repository_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/repository_dependencies.xml Thu Jan 22 09:08:45 2015 -0500
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diff -r 000000000000 -r 0624d484adba snpSift_dbnsfp.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/snpSift_dbnsfp.xml Thu Jan 22 09:08:45 2015 -0500
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+
+ Add Annotations from dbNSFP and similar annotation DBs
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+ snpSift_macros.xml
+
+
+ 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
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+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@
+
+
+
+
diff -r 000000000000 -r 0624d484adba snpSift_macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/snpSift_macros.xml Thu Jan 22 09:08:45 2015 -0500
@@ -0,0 +1,35 @@
+
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+ snpEff
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+For details about this tool, please go to:
+ http://snpeff.sourceforge.net/SnpEff_manual.html
+
+
+ ------
+
+**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.
+
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+ 10.3389/fgene.2012.00035
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diff -r 000000000000 -r 0624d484adba 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 09:08:45 2015 -0500
@@ -0,0 +1,10 @@
+##fileformat=VCFv4.1
+##samtoolsVersion=0.1.18 (r982:295)
+##INFO=
+##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=
+#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)
diff -r 000000000000 -r 0624d484adba 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 09:08:45 2015 -0500
@@ -0,0 +1,15 @@
+##fileformat=VCFv4.1
+##samtoolsVersion=0.1.18 (r982:295)
+##INFO=
+##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=
+##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=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+#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
diff -r 000000000000 -r 0624d484adba test-data/test_dbnsfpdb.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_dbnsfpdb.tabular Thu Jan 22 09:08:45 2015 -0500
@@ -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 . . . . . . . . . . . . .
diff -r 000000000000 -r 0624d484adba 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 09:08:45 2015 -0500
@@ -0,0 +1,3 @@
+#id build description path annotations
+#GRCh37_dbNSFP2.4 GRCh37 GRCh37 dbNSFP2.4 /depot/snpeff/ SIFT_pred,Uniprot_acc
+#GRCh38_dbNSFP2.7 GRCh38 GRCh38 dbNSFP2.7 /depot/snpeff/ SIFT_pred,Uniprot_acc
diff -r 000000000000 -r 0624d484adba 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 09:08:45 2015 -0500
@@ -0,0 +1,7 @@
+
+