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Archive of entries posted on February 2012

1000 genomes is so yesterday

Genotypes frequencies of the popultation are the most powerfull filter for rare mutations, we all know that. That’s also why we had the genotype frequency filter that was based on the 1000 genomes data right from the beginning. If you set this filter to let’s say 0.5 you reduced your vcf file to genotypes that [...]

How do we filter positions on the X and Y chromosome?

Males are hemizygous for the X and Y chromosome, thus the concept of diploid genotypes does not apply here. However, all common variant callers are currently dealing with these positions as if they were diploid. This means in vcf format a hemizygous variant on a male X chromosome would be reported as if it were [...]

New: Ratings and comments for annotations

We introduced some kind of second-level annotation: You can add comments to annotations, stating that you agree, disagree, like to know more, or just express your interest in a certain disease that is already annotated in GeneTalk. In addition, you can rate annotations for ‘trustworthy’ and ‘disease-causing’. With this ratings, the GeneTalk community will be [...]

Hidden fields in rails (or: sometimes rails sucks)

Well, in general, ruby on rails is a powerful tool for developing web applications. But sometimes it really sucks, because of inconsistencies in the API. I tried to add a hidden field to a form_for. A hidden field for form_tag works like: So for form_for forms, I expect (similar to text_field etc.): But this solution [...]

Understanding Filters in GeneTalk

To understand the results of VCF-file filtering and to choose your filter parameters appropriately, it might help to know how the filters in GeneTalk work. The flowchard attached to this post gives an overview on the filtering process in GeneTalk.   Click image to enlarge.

News

In the last weeks, we worked on a number of features and improvements. The most important new feature is the Inhertiance Filter for VCF files which allows you to filter your VCF file for dominant, homozygous recessive, or compound heterozygous genotypes (see the screenshot below). Other new features include: An overview for the selected filter [...]

Our Preferred Reference Sequence

You might remember Einstein telling you that there is no preferred inertial reference frame. So wrong that guy! We definitely prefer GRCh37 for the human reference sequence! GRCh37 or hg19 is the latest build and its coordinate system is probably not going to change anymore. Updates are rather released as patches [1]. We therefore use [...]