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Sage-Bionetworks / Genie

Validation and processing of GENIE files
https://genie.synapse.org/
MIT License
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MAF file validation #512

Open jakevc opened 1 year ago

jakevc commented 1 year ago

After fining out that we were submitting incorrect MAF formatted variants for the ERBB2 and EGFR insertions, I realized it would be easy to catch this in validation with some simple rules about the ref and alt allele that would force the correct MAF format for insertions as well as deletions:

https://docs.gdc.cancer.gov/Data/File_Formats/MAF_Format/

Pseudo Code for test: ValidateInsertion: If mutation.is_insertion: require(Reference_Allele=='-') ValidateDeletion: If mutation.is_deletion: require(Tumor_Seq_Allele2="-")

thomasyu888 commented 1 year ago

Thanks @jakevc . We are tracking this internally on Jira: https://sagebionetworks.jira.com/browse/GEN-582. But will leave this open to update you.