Truth sets for variant calling validation

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6.5 years ago

filippo.martignano ▴ 20

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?

variant calling validation truth sets • 2.1k views

ADD COMMENT • link updated 6.5 years ago by Kevin Blighe 87k • written 6.5 years ago by filippo.martignano ▴ 20

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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 REPLY • link 6.5 years ago by WouterDeCoster 47k

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~~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 REPLY • link 6.1 years ago by Kevin Blighe 87k

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