Type

Choose type of variant: single nucleotide polymorphisms (SNPs) and/or indels. Selecting indels also displays MNPs and mixed type variants.

Alternate Allele Frequency in this analysis

Limit variants using a threshold for the allele frequency within a phenotypic group. For example, you may want to display only variants that are common in one group, but rare or absent in another.

Minor Allele Frequency in the general population

Exclude variants that occur in greater than 5% of the population in public data sets (1000 Genomes and HapMap).

Minimum Conservation Score

Exclude variants that have a conservation score below this threshold. A conservation score indicates how conserved a nucleotide is at a position across a group of related organisms. For humans we use the primate subset of the 46-way phastCons scores calculated by the UCSC Genome Bioinformatics Group. Setting a threshold will exclude those variants at positions lacking a conservation score.

Regions

Limit results to variants that occur in particular genomic regions (eg. chr20:55550-70000). Multiple entries can be submitted simultaneously. Each additional entry should be on a new line.

Gene

Limit results to variants that affect specified genes. Supply gene symbols from the gene model source selected when the analysis was begun (Ensembl or RefSeq). Each additional entry should be on a new line.

Effect Severity and Category

Limit results to include only variants of specified severity levels or within particular subcategories.

Quality

Set a minimum threshold for variant quality as determined by the variant calling pipeline.

Effect

Effect severity on affected gene(s). May include multiple effects due to potential impact on more than one gene or transcript. Details are displayed when the mouse hovers over the column. For definitions of effects see SnpEff documentation at (http://snpeff.sourceforge.net/SnpEff_manual.html).

Conservation

A conservation score indicates how conserved a nucleotide is at a position across a group of related organisms. For humans we use the primate subset of the 46-way phastCons scores calculated by the UCSC Genome Bioinformatics Group.

Public MAF

Indicates variants that occur in greater than 5% of the population in public data sets like 1000 Genomes and HapMap.