PLINKSEQ browser

Example 1000 Genomes phase 1 dataset (16-Mar-2012 release); RefSeq coding variants extracted

This dataset

This dataset represents the "whole-exome" subset of variants from the 1000 Genomes phase 1 (16-March-2012) release.

General overview and instructions

This table browser is designed to provide easy access to any PLINK/Seq project, which consists of one or more VCF files (with variant and genotype data, including extenisble, typed meta-data) and several core reference databases (gene, sequence and variant databases such as RefSeq, CCDS, hg18 human sequence, dbSNP, and the 1000 Genomes Project data). This particular browser is oriented towards exome studies, with a gene-centric focus.

The main page contains the following fields:

Gene ID

This is the main input field. Enter here either one or more gene symbol (e.g. ANK3), RefSeq NM number or a region (e.g. chr22:17000000..19000000). If there is more than one transcript for a gene, these will be listed, and you can select a specific one. You can click on list to get a list of all gene symbols in the database.

The format should be 1 entry per row: either gene name, or NM number, or a range, with 1 or 2 base positions, e.g.

   chr1:12345..67890
   ANK3
   chr2:787882
   NM_012345
i.e. the 3rd row specifies a single position. If no variant exists here, it will be ignored. (In future, an rs-based lookup will be added.)

Gene set

This specifies the gene/transcript database used by the browser. By default this is set to a RefSeq table, that is indexed by both NM numbers for transcripts as well as gene symbols. Do not edit this field for now.

Variant meta-fields

These are the extensible set of fields that were present in the VCF files uploaded into the project. Click on list to see all available fields. If you type the keywords here, then they are appended in the table. For example, type (space delimited) 

    proteinchange type DB
(case sensitive) to get info on the nature of the variant, and a flag for dbSNP membership.

To append all available variant meta-fields, enter an asterisk (*) in this box.

Phenotype

If phenotype data are available for the individuals, it can be specified here. Currently, only case/control phenotypes are supported. In the gene-table output, a case/control count will be appended to each variant (numbr of non-reference genotypes). In the individual-view, a CASE or CONTROL label will be appended next to each individual/genotype.

Mask specification

Any valid mask statement can be specified here.

Include filters

An include filter can be specified here. This is equivalent to entering include="...expression..." in the mask field, but avoids potential issues in parsing the quoted expression, etc.

Output

This should hopefully be fairly self-explanatory. There are 3 main views:

  • Gene view: This page lists all variants in a gene or transcript. If additional regions and/or genes are specified, these are listed also. Note that exon numbering is currently not with respect to strand orientation of the gene.

  • Variant view: This lists detailed variant information and all meta-fields for a single variant; also list all genotypes for individuals (sorted by genotype) for this variant. Obtained by clicking on view in the gene table for a particular variant.
  • Individual view: Lists all variants and genotypes for a particular individual for the key single gene queried. Obtained by clicking on the individual ID field in the variant table for a particular person.