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monarch-initiative / dipper

Data Ingestion Pipeline for Monarch
https://dipper.readthedocs.io/en/latest/
BSD 3-Clause "New" or "Revised" License
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iscn parser util #77

Open nlwashington opened 9 years ago

nlwashington commented 9 years ago

we need to be able to deal with complex rearrangements encoded with ISCN notation. the handbook is here:

http://onlinelibrary.wiley.com/doi/10.1002/0471142905.hga04cs17/pdf

we'll need to be able to parse the standard forms of ISCN notation, and then map them into the GENO model. Coriell cell lines are a good resource for this, where the 'karyotype' column lists the ISCN notation for the genotype.

nlwashington commented 9 years ago

there are some resources here: http://cydas.org/Resources/ but none seem simple for us to leverage.

nlwashington commented 9 years ago

we may be able to leverage the services http://cydas.org/OnlineAnalysis/Service.asmx