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Validated CNV dataset for NA12878

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.

ngs cnv
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updated by Ram Ram • written by thecuriousbiologist thecuriousbiologist

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

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updated by Ram Ram • written by stefan.mester • stefan.mester

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

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updated by Ram Ram • written by User 59 User 59

2 answers

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.

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updated by Ram Ram • written by donfreed donfreed

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

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updated by Ram Ram • written by Zev.Kronenberg Zev.Kronenberg

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