variant filtering and annotation

[krawitz]

Are you looking for a needle in a haystack? Well, GeneTalk might help you with filtering and annotating your sequence variants:

http://www.youtube.com/watch?v=z1TqiXP-gEo

[krawitz]

If you click on the more button in the vcfViewer in GeneTalk you can see the HGVS code of the variant and are linked to the MutationTaster prediction:

http://youtu.be/xx1JiZkdAB0

[krawitz]

If you set the annotation filter, you will get all variants in your vcf file that have a GeneTalk User annotation or a scientific article linked to the specific mutation

[krawitz]

Hi,
we really had quite a high server load after these posts, so GeneTalk crashed several times over the last three days. However, now we scaled up the hardware (three servers in parallele) and all new users should be able to get their data filtered in a few seconds again,...

[krawitz]

removing artefacts from variant list

In the 1000 genomes project more than 7 Mio variant calls were classified as probably false positives. These artefact positions are now marked by a lightning in GeneTalk (www.gene-talk.de) and can be filtered out.

In a usual exome we filter out between 1-2% of the variants based on this blacklist. Many of these artefacts don't have dbSNP IDs yet. Thus removing these artefacts might really speed up your NGS analysis!