Skip to content
Archive of posts filed under the Tutorials category.

Where have all the annotations gone?

Where have all the annotations gone? Long time passing. Where have all the annotations gone? Long time ago. Where have all the annotations gone? The stars show ratings now! When do they ever learn? When do they ever learn? I hope, the last line does apply to us and our attempts to make GeneTalk more [...]

GeneTalk becomes an assembly-line worker

GeneTalk now helps you when you have a bunch that have to be filtered with the same filter settings. We added two features for supporting such batch processing: You can upload a ZIP-file containing serveral VCF files. GeneTalk will unpack your ZIP-file and add all VCF files to your account When selecting an individual for [...]

All theory, dear friend, is grey and the golden tree of life springs ever green,…

You are absolutely right, Mephistopheles. That’s why we uploaded exomes of a CEU Trio to the Demo account, so that you can play around with the new segregation filter! It is a well described Trio from the 1000 genomes paper: NA12787 is the daughter, NA12892 is the mother and NA12791 is the father. In the [...]

New: Segregation Filter

GeneTalk now supports coupled filtering of two or more individuals! The first step is to create a new VCF file that contains all the individuals or, if you already uploaded a such a file, enter the phenotype information for your file. You can create a file with multiple individuals by using the new function “Create [...]

tutorial

It’s right after lunch and you are bored to read about the postprandial hypoglycemia of your facebook friends? Well then, grab a coffee instead and watch this invigorating tutorial!

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 [...]

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.

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 [...]

Demo user

For all users that do not yet have a vcf file of an exome right at hand, there is the demo account. Just log in with user: demo password: demodemo In the My VCF files there is one European and one African exome that we took from the 1000 genomes project (ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/VCF/v4.0/). You can play [...]