Validated CNV dataset for NA12878

Question

[thecuriousbiologist]

Hi, I was wondering if anybody could point me to public datasets having validated CNV calls from NGS for the Corriell sample NA12878.

I found this old thread, which says that there is not a standard CNV set available, however the thread is 3.5 years old and I am wondering if there were any sets compiled after that and which are available now.

Any help would be much appreciated.

Thank you.

[User 59]

Does this have to be CNV calls from NGS? What is wrong with an array based dataset in this instance? http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0027859#s5

[stefan.mester]

Thanks for the link! really like the curated set of deletions!

[User 59]

Please don't append comments/thanks as answers..

Answer 1

[donfreed]

See the LUMPY paper. The authors do a good job using many available validated SV call sets for NA12878 (including from NGS data). Many sets of validated SV calls are available as supplementary files.

Answer 2

[Zev.Kronenberg]

You can also use the Phase3 SV calls from the 1Kg genome project.