Updated analysis: assess CNV amplification and deep deletion threshold in TARGET and GMKF data

[jharenza]

What analysis module should be updated and why?

focal-cn-preparation

Either before or once v7 is released, assess amplification threshold of TARGET WXS CNVs using MYCN status (molecular_subtype). Typically, MYCN amplification is called when there are 8-10+ copies of the gene and our current amplification thresholds may be a bit low for this. So, assess what is called vs what is subtyped as amplified or non-amplified.

For deep deletions, we can assess CDNK2A for ALL (though this piece will come in v8).

What changes need to be made? Please provide enough detail for another participant to make the update.

See above

What input data should be used? Which data were used in the version being updated?

Consensus CNV file, histologies file

When do you expect the revised analysis will be completed?

1-2 weeks

Who will complete the updated analysis?

@kgaonkar6

[jharenza]

assigning to @ewafula cc @afarrel

@ewafula you can make a branch off of this PR to work on this: d3b-center/OpenPedCan-analysis#89

[taylordm]

Next step: Wait for new CNV method comparison by Alvin, can run multi-CNV on NB data , and do the same comparison with the old CNV calls. In progress with Brian E.

[jharenza]

This was addressed in d3b-center/OpenPedCan-analysis#264