This page presents options for defining global filters based on variant properties such as number of reads and frequency in the population.

It also presents options for searching for variants in both the curated somatic variants dataset and the full Beat AML dataset.

Filters set here will affect the data shown in all views that display and/or export variants.

DNA variant search
Enter a gene name to query the DNA variant database for all variants in that gene, or enter a gene name and an amino acid change to query for a specific variant within that gene.

This query will return all possible variants, regardless of global filters, so can be a helpful check if you're not seeing a variant elsewhere in Vizome, but were expecting to.

The search results are presented in a table, with each row corresponding to a different variant type. All results of the same variant type are concatenated into the same row, with a total number of samples displayed in the first column.

Search results also include ref, alt, chromosome, start position, end position, amino acids, protein position, frequency across samples, allele frequency range, frequency in OHSU AML normals, presence in dbSNP, presence in COSMIC, ExAC MAF, and tumor only indicator. Again, these values are concatenated for many variants and samples, so to focus on specific variants, other Vizome views will be useful.

Cohort variant frequency
A minimum or maximum population frequency (or both) can be set as a global filter. Each variant has a calculated value for frequency across all samples. These values do not change, and they are used to include or exclude variants when this global filter is set. For example, to restrict your data to variants found in at least 10% of the sample population, set the minimum to 10 and leave the maximum at 100. This filter affects the data shown in all views that display and/or export variants.

Number of reads
A minimum number of reads can be set as a global filter. In the AML database, each variant already has a read count greater than five, so the filter cannot be set to a value less than five. By default, this filter does not operate with a maximum, meaning it will not exclude any variants with more than a certain number of reads. You may elect to change this by checking the box labeled "Limit maximum reads" and then entering a number value in the "Max reads" box. This filter (whether minimum or maximum or both) affects the data shown in all views that display and/or export variants.

Variant allele frequency
A minimum variant allele frequency can be set as a global filter. This is the frequency found by dividing the number of alternative allele reads by the number of total reads for a single variant found in a single sample. Minimum should be entered here as a percentage. This filter affects the data shown in all views that display and/or export variants.

Variant types
Variant types can be included or excluded with the checkboxes shown. Each variant has one value for "variant type," and those values are used to include or exclude variants when this global filter is set. This filter affects the data shown in all views that display and/or export variants.