Question: Truth sets for variant calling validation
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gravatar for filippo.martignano
17 months ago by
filippo.martignano10 wrote:

Hi everyone!

I was looking for validated truth sets in order to test my custom pipeline for variant calling.

I've already found the ICGC-TCGA DREAM truth sets ( https://www.synapse.org/#!Synapse:syn312572/wiki/62018 ), and the genome in a bottle truth sets (http://jimb.stanford.edu/giab).

Can you suggest me additional sets?

ADD COMMENTlink modified 17 months ago by Kevin Blighe39k • written 17 months ago by filippo.martignano10

The NA12878 (human), among other samples, has been characterized by virtually every technology on the planet (Genome in a bottle project). So you should be able to find a truth set for that genome.

ADD REPLYlink written 17 months ago by WouterDeCoster37k

Hey Filippo, the ICGC set looks perfectly fine.

Obviously, the ideal situation is to perform 'in house' validation against a gold standard. In clinical genetics laboratories, the gold standad is still Sanger di-deoxy sequencing.

ADD REPLYlink modified 11 months ago • written 17 months ago by Kevin Blighe39k
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