Add a script to filter mutations in a MAF file #66
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I am a bit puzzled by finding Validation_Status set to Wildtype.
Typically, only Mutation_Status is marked as Wildtype, not Validation_Status.
It seems redundant since records with Mutation_Status=Wildtype are already filtered out by MutationFilter.
If there are messy records that do have Validation_Status=Wildtype we should consider accepting only records that
have Validation_Status values among valid ones {Valid, Unknown, Not Valid, Untested, Redacted?}
This script uses the same filters that are used during the load (except filter by gene that required connection to the database)
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Enhance the cBioPortal loader by reusing the existing filters, except for gene matching, which requires a database connection.
This script generates a fully matching MAF file for complete and successful database loading. It is recommended to run the validator in strict mode to identify any genes in the MAF file that are absent from the database.