Showing posts from April, 2018

Excluding variants from search based on Patient study codes

When doing our own variant analysis, we often seek variants that shared between affected individuals, and we already provide this capability using the 'shared' filter. We recently added a new filter to take this search one step further by removing variants found in the unaffected individuals (usually from the same family). There is a new textbox called 'Exclude variants' where users can add patient study codes to exclude the variants found in these individuals from the variants found in the other individuals in a single search operation. Keep in mind, that each person will carry thousands of variants, so filtering in this way can be quite slow if no other filters are applied. So it is recommended that users apply as many filters as possible to narrow the search before using this functionality.

GnomAD ethnic frequencies exportable

We've added a new option for users to export GnomAD ethnic frequencies to excel which includes south asian, east asian, african american, jewish, non-finnish european, finnish and other minor allele frequencies (MAF). It's optional because we don't actually store the gnomAD frequencies in our database and have to fetch them from elsewhere making export slower especially when exporting thousands of variants. It's best to filter as much as you can before enabling this option.

Affected statuses: Database vs Pipeline

We recently introduced a new filter called 'Pipeline affected status'. This is not be confused with the other 'Affected status' or 'Disease status' filter which is taken from our Patient Database. The 'Pipeline affected status' differs such that you can reconfigure the pipeline to use a different affected status from what is set in the database to produce different cohort reports. This is useful in cases when the affected status applies to multiple phenotypes or diagnoses and you want to to do repeated cohort analysis under different conditions.