Click 'Add Files' to select files to upload from your local file system. A maximum of 24 files of 400 MB can be uploaded at once.
Please make sure to select the correct file type. All files in the upload must have the same file type.

File Type	Agilent Interval Report File Generic File PennCNV output file VCF File

Add files... Start upload Cancel upload

 

Filename	Size	Status	Progress / Warnings	Actions

Click 'Next' to continue with associating the samples in the files to patient records. If you do not want to associate the files and samples at this time, click 'Finish'.

Use the status and version selections on the available annotation sources and the status selections on the individual annotations per source to select a source for each variant annotation. Once saved, the configuration is immediately active for all newly created Analyses.

Name	Status	Version	Description	Info
1000Genomes	enabled disabled	1	1000 Genomes Phase1 release v3.20101123	Show external sources Show annotations
External Sources Name Version URL 1000 Genomes hg19_phase1_release_v3.20101123 ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20110521/ALL.wgs.phase1_release_v3.20101123.snps_indels_sv.sites.vcf.gz
Annotations Category Name Display Name Status Population 1000Gp1_FreqAll 1000 genomes phase 1 allele frequency all enabled disabled Population 1000Gp1_FreqAFR 1000 genomes phase 1 allele frequency African enabled disabled Population 1000Gp1_FreqEUR 1000 genomes phase 1 allele frequency European enabled disabled Population 1000Gp1_FreqAMR 1000 genomes phase 1 allele frequency American enabled disabled Population 1000Gp1_FreqASN 1000 genomes phase 1 allele frequency Asian enabled disabled
DataFile	enabled disabled	1	Annotations derived from the input datafile records.	Show external sourcesShow annotations
External Sources Name Version URL VCF (Variant Call Format) 4.1 http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41
Annotations Category Name Display Name Status Quality infoAF Allele frequency enabled disabled Quality infoAD Allelic depth enabled disabled Quality infoDP Read depth enabled disabled Quality quality Call quality enabled disabled Quality infoGQ Genotype quality enabled disabled Quality infoMQ Mapping quality enabled disabled Quality filter Filter status enabled disabled
dbNSFP	enabled disabled	2 1	dbNSFP v2.0: Database of functional predictions for non-synonymous SNPs	Show external sourcesShow annotations
External Sources Name Version URL dbNSFP 2.0 https://sites.google.com/site/jpopgen/dbNSFP dbNSFP paper Human Mutation. 32:894-899 http://onlinelibrary.wiley.com/doi/10.1002/humu.21517/abstract
Annotations Category Name Display Name Status Conservation SLRSelection SLR selection score enabled disabled Missense SIFTweight SIFT score enabled disabled Missense PPH2HumDivScore PolyPhen2 score HumDiv enabled disabled Missense PPH2HumVarScore PolyPhen2 score HumVar enabled disabled Missense PPH2HumDivPrediction PolyPhen2 prediction HumDiv enabled disabled Missense PPH2HumVarPrediction PolyPhen2 prediction HumVar enabled disabled Coding LRTscore LRT score enabled disabled Coding LRTprediction LRT prediction enabled disabled Coding LRTomega LRT omega enabled disabled Substitution MutationTasterScore MutationTaster score enabled disabled Substitution MutationTasterPrediction MutationTaster prediction enabled disabled Conservation gerpPPNeutralRate GERP++ neutral rate enabled disabled Conservation gerpPPRSScore GERP++ RS score enabled disabled Conservation phyloP PhyloP score enabled disabled Conservation SiPhyScore SiPhy score enabled disabled Substitution MutationAssessorScore MutationAssessor score enabled disabled Substitution MutationAssessorPrediction MutationAssessor prediction enabled disabled Substitution FATHMMScore FATHMM Score enabled disabled
dbNSFP	enabled disabled	2 1	dbNSFP v2.0b3: Database of functional predictions for non-synonymous SNPs	Show external sourcesShow annotations
External Sources Name Version URL dbNSFP 2.0b3 https://sites.google.com/site/jpopgen/dbNSFP dbNSFP paper Human Mutation. 32:894-899 http://onlinelibrary.wiley.com/doi/10.1002/humu.21517/abstract
Annotations Category Name Display Name Status Conservation SLRSelection SLR selection score enabled disabled Missense SIFTweight SIFT score enabled disabled Missense PPH2HumDivScore PolyPhen2 score HumDiv enabled disabled Missense PPH2HumVarScore PolyPhen2 score HumVar enabled disabled Missense PPH2HumDivPrediction PolyPhen2 prediction HumDiv enabled disabled Missense PPH2HumVarPrediction PolyPhen2 prediction HumVar enabled disabled Coding LRTscore LRT score enabled disabled Coding LRTprediction LRT prediction enabled disabled Coding LRTomega LRT omega enabled disabled Substitution MutationTasterScore MutationTaster score enabled disabled Substitution MutationTasterPrediction MutationTaster prediction enabled disabled Conservation gerpPPNeutralRate GERP++ neutral rate enabled disabled Conservation gerpPPRSScore GERP++ RS score enabled disabled Conservation phyloP PhyloP score enabled disabled Conservation SiPhyScore SiPhy score enabled disabled
dbSNP	enabled disabled	1	dbSNP build 137	Show external sourcesShow annotations
External Sources Name Version URL dbSNP 137 http://www.ncbi.nlm.nih.gov/projects/SNP
Annotations Category Name Display Name Status ID rsValidated dbSNP validated enabled disabled ID rsHeterozygosity dbSNP average heterozygosity enabled disabled ID rsBuildCreated dbSNP build created enabled disabled ID rsBuildUpdated dbSNP build last updated enabled disabled ID rsSuspectFalse dbSNP suspect false snp enabled disabled ID rsClinicalSignificance dbSNP clinical significance enabled disabled ID rsAlleleOrigin dbSNP allele origin enabled disabled Population rsMAF dbSNP global Minor Allele Frequency enabled disabled
ESP6500	enabled disabled	2 1	Variants in the ESP6500SI-V2 dataset of the exome sequencing project (ESP), annotated with SeattleSeqAnnotation137.	Show external sourcesShow annotations
External Sources Name Version URL Exome Variant Server ESP6500SI-V2 dataset v.0.0.20. (June 7, 2013) http://evs.gs.washington.edu/EVS/ SeattleSeq 8.05 http://snp.gs.washington.edu/SeattleSeqAnnotation137/
Annotations Category Name Display Name Status Conservation gerpConsScore GERP conservation score enabled disabled Conservation phastCons PHAST conservation score enabled disabled Conservation granthamDist Grantham distance enabled disabled Missense PPH2prediction PolyPhen2 prediction enabled disabled Population ESP6500_alleleFrequencyAll ESP6500 allele frequency all enabled disabled Population ESP6500_genotypeFrequencyAll ESP6500 genotype frequency all enabled disabled Population ESP6500_alleleFrequencyEA ESP6500 allele frequency European American enabled disabled Population ESP6500_genotypeFrequencyEA ESP6500 genotype frequency European American enabled disabled Population ESP6500_alleleFrequencyAA ESP6500 allele frequency African American enabled disabled Population ESP6500_genotypeFrequencyAA ESP6500 genotype frequency African American enabled disabled
ESP6500	enabled disabled	2 1	Variants in the ESP6500 dataset of the exome sequencing project (ESP), annotated with SeattleSeq.	Show external sourcesShow annotations
External Sources Name Version URL Exome Variant Server ESP6500 dataset v.0.0.14. (June 20, 2012) http://evs.gs.washington.edu/EVS/ SeattleSeq 7.05 http://snp.gs.washington.edu/SeattleSeqAnnotation134/
Annotations Category Name Display Name Status Conservation gerpConsScore GERP conservation score enabled disabled Conservation phastCons PHAST conservation score enabled disabled Conservation granthamDist Grantham distance enabled disabled Missense PPH2prediction PolyPhen2 prediction enabled disabled Population ESP6500_alleleFrequencyAll ESP6500 allele frequency all enabled disabled Population ESP6500_genotypeFrequencyAll ESP6500 genotype frequency all enabled disabled Population ESP6500_alleleFrequencyEA ESP6500 allele frequency European American enabled disabled Population ESP6500_genotypeFrequencyEA ESP6500 genotype frequency European American enabled disabled Population ESP6500_alleleFrequencyAA ESP6500 allele frequency African American enabled disabled Population ESP6500_genotypeFrequencyAA ESP6500 genotype frequency African American enabled disabled
HGMDProfessional	enabled disabled	2 1	HGMD® Professional Database 2013.2	Show external sourcesShow annotations
External Sources Name Version URL Biobase HGMD® Human Gene Mutation Database 2013.2 http://www.biobase-international.com/product/hgmd
Annotations Category Name Display Name Status ID hgmdAccession HGMD accession number enabled disabled ID hgmdPMID HGMD PubMed reference enabled disabled HGMD® hgmdConfidence HGMD Confidence enabled disabled HGMD® hgmdMatch HGMD Match enabled disabled HGMD® hgmdMutationType HGMD Mutation type enabled disabled HGMD® hgmdVariantType HGMD Variant type enabled disabled HGMD® hgmdDisease HGMD Disease enabled disabled
HGMDProfessional	enabled disabled	2 1	HGMD® Professional Database 2012.4	Show external sourcesShow annotations
External Sources Name Version URL Biobase HGMD® Human Gene Mutation Database 2012.4 http://www.biobase-international.com/product/hgmd
Annotations Category Name Display Name Status ID hgmdAccession HGMD accession number enabled disabled ID hgmdPMID HGMD PubMed reference enabled disabled HGMD® hgmdConfidence HGMD Confidence enabled disabled HGMD® hgmdMatch HGMD Match enabled disabled HGMD® hgmdMutationType HGMD Mutation type enabled disabled HGMD® hgmdVariantType HGMD Variant type enabled disabled HGMD® hgmdDisease HGMD Disease enabled disabled
HGMDPublic	enabled disabled	3 2 1	HGMD® Public Database 2013.2	Show external sourcesShow annotations
External Sources Name Version URL Biobase HGMD® Human Gene Mutation Database 2013.2 http://www.biobase-international.com/product/hgmd
Annotations Category Name Display Name Status ID hgmdAccession HGMD accession number enabled disabled
HGMDPublic	enabled disabled	3 2 1	HGMD® Public Database 2012.4	Show external sourcesShow annotations
External Sources Name Version URL Biobase HGMD® Human Gene Mutation Database 2012.4 http://www.biobase-international.com/product/hgmd
Annotations Category Name Display Name Status ID hgmdAccession HGMD accession number enabled disabled
HGMDPublic	enabled disabled	3 2 1	HGMD® Public Database 2012.2	Show external sourcesShow annotations
External Sources Name Version URL Biobase HGMD® Human Gene Mutation Database 2012.2 http://www.biobase-international.com/product/hgmd
Annotations Category Name Display Name Status ID hgmdAccession HGMD accession number enabled disabled

Configuration errors

Following variant annotations have more than one source identified, please select only one source by disabling the others in their respective annotation sources.

Annotation	Selected in
hgmdAccession	HGMDProfessional, HGMDPublic

Warning

Following variant annotations have no source identified. These annotations will not be populated in new Analyses and therefore not be available for visualization or triage & classification. This does not prevent the configuration from being saved.

Annotation	Available in