Which tool do I use for .... ?

  1. I have 3000 variant calls. How do I find out which is possibly significant? - Use Variation Reporter.
  2. I am studying my favorite gene. How do I find all variants on that gene? - Use Variation Viewer.
  3. I want to know if my variant has been observed in the 1000 Genomes study. - Use the 1000 Genomes Browser.
  4. I have a VCF file in GRCh37 coordinates.  How do I move those to GRCh38 coordinates? - Use the NCBI Genome Remapping Service.
  5. I want to search the NHGRI GWAS Catalog for studies related to Basal Cell Carcinoma. - Use PheGenI.

NCBI Variation Tools

This is a list of available NCBI Variation Tools for investigating and understanding human variation.

Variation Reporter

Variation Reporter matches user-provided locations (in VCF, GVF, BED or HGVS format) in NCBI Variation Databases (dbSNP, dbVar and ClinVar) and reports molecular consequences and clinical attributes .  When no match is found, the report includes a prediction of the molecular consequence of the variant, based on the NCBI annotation data for the target genome assembly chosen by the user.  It supports data uploading and reporting on GRCh37.p13 or GRCh38.  Use the Variation Reporter API for bulk processing.  More information can be found on the NCBI Variation Reporter fact sheet.

Variation Viewer

Variation Viewer is a tool for interactive examination and download of nucleotide variants for a specific locus.  It supports both the GRCh38 and GRCh37.p13 assemblies.  Variation Viewer integrates data from all of the NCBI Variation databases and presents them in a coupled graphical and tabular report.  The resulting list of variants can be saved locally using the download function.  You can also upload their own variant data to this browser.  More information can be found on the NCBI Variation Viewer Fact sheet and in an introductory video tutorial.

1000 Genomes Browser

1000 Genomes Browser allows you to review sequence alignments and variant calls from the 1000 Genomes Project in the context of various genome annotations.  Browse data by population or individual sample, as well as by sequencing platform, aligner or experiment type.  Download genome slices of sequence and alignment data or genotype calls.  Users can also upload their own data into the browser.  All data is displayed in GRCh37.p13 coordinates.

NCBI Genome Remapping Service

The NCBI Genome Remapping Service is a tool that projects users' annotation data from one coordinate system to another.  With the Assembly-Assembly remap, you can remap your variant calls between different assembly versions, while the Clinical Remap permits you to remap data between RefSeqGenes or LRGs and an assembly, using NCBI calculated alignments. More information can be found on the NCBI Remap Service fact sheet.  The remapping service has a web interface as well as an API for bulk processing.

PheGenI

The Phenotype-Genotype Integrator (PheGenI) is a tool that integrates the search and retrieval of associated genotype-phenotype data from National Human Genome Research Institute (NHGRI) Genome-wide Association Study (GWAS) Catalog integrated with data housed in Gene, dbGaP, OMIM, GTEx and dbSNP.   It provides search by genotype and phenotype.  The dbSNP Data in NCBI PheGenI is only mapped GRCh38 at this time.  More information can be found on the NCBI Phenotype-Genotype Integrator fact sheet.

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Last updated: 2014-10-15T11:55:28-04:00