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Snitkin-Lab-Umich / scripts

Frequently used Scripts
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WARNING_TRANSCRIPT_NO_START_CODON" #29

Open katiesaund opened 5 years ago

katiesaund commented 5 years ago

https://github.com/Snitkin-Lab-Umich/scripts/blob/bd327744ca96acad0a3084c504bd1ae80f76c565/variant_parser_functions.R#L67

How do we want to deal with variants that say WARNING_TRANSCRIPT_NO_START_CODON? We should look into which genes cause this message and then decide how to handle within the parser.

katiesaund commented 5 years ago

Some of the genes in my matrix (ex: CD630_00040) have variants with the WARNING_TRANSCRIPT_NO_START_CODON, but other variants (same gene) have normal annotations. what is causing this problem?

katiesaund commented 5 years ago

Actually, I looked at a specific variant in this gene, Asn352Asp, and found that it has the "WARNING_TRANSCRIPT_NO_START" error in the two VCF files in the snpeff output but that is not included in the snpmat row name. Same with other variants in this gene so I don't think SNPeff is being inconsistent -- (it's wrong, for sure, but not inconsistent).