WARNING: Discrepancy in SNP at position 58089821 of chr 12
Issue #6
resolved
Hi,
oncoFML outputs several warnings like this "WARNING: Discrepancy in SNP at position..." when I am using a custom score function (tabix indexed).
What are the possible causes? Can we ignore these?
Additional details:
OncodriveFML version 2.0.3
The same mutation file produces no warning with CADD scores.
The output results make sense, we get known drivers.
Our score function is only defined on the CDS of protein_coding transcripts.
Thank you
Comments (3)
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assigned issue to
Iker Reyes
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assigned issue to
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- changed status to resolved
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The reason you get that warning when using your custom scores is because the reference nucleotide of that mutation is not the same as the one in the reference genome for that position, or because your tabix file lacks for that position the particular alternate nucleotide you have in the mutation file.
OncodriveFML will just ignore that mutation in the analysis, for the rest it will work as expected.