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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 user friendly. The “Show Annotations” button in the VCF file view was replaced by a more informative view: Now, you see the topmost rankings of the annotations for a variant. The two rows of stars show the highest ranking in medical relevance and scientific evidence. Moreover, a flag that shows if there are experts for this variant (shown by a ‘doctor icon’ following the stars; see screenshot). Just click on the stars an you will see the annotations.

There’s one more thing.

You can now filter your VCF files for annotations with certain ratings. In the “Annotation Filter” tab of the filter settings, you see (amongst others) one row of stars for medical relevance and one for scientific evidence. With these rows you choose that a variant must have annotations with at least these ratings to be shown in the filtered file. Variants that have no annotation are treated differently: The third row of stars lets you choose, whether you want to keep those variants in the filtered file or not.

Let me give you an example: You want to remove all variants with a “blacklist” annotation from your VCF file. You set “medical relevance” to two stars (“suspicious”) and “Keep all variants without annotation”. Thus, every variant that has just annotations with one star in medical relevance (“irrelevant or artifact”) are sorted out.

Using the fourth row of stars, you can filter out variants for which there is no expert in GeneTalk.

More annotation filters will come soon.

One Comment

  1. young girls says:

    come on, tom, you have picked them, but you did very well!

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