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Old 06-21-2016, 01:47 PM   #1
anjulka
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Location: Cambridge, MA

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Default MNV nomenclature in VCFs

We have been using GATK readbackphasing to phase multinucleotide variants in our generated data. The output from this walker just reports the bases affected by substitutions. However, we just noticed that we were not getting Cosmic annotation for a number of these, as Cosmic MNVs are reported with the preceding base in both the REF and ALT allele.

For example, in our vcfs, a MNV is represented as: chr7 140453135 CA TT (This is an MNV leading to BRAF V600E). The Cosmic count is NA.
In the COSMIC vcf, the same variant is chr7 140453134 TCA TTT ID=COSM475 and CNT=55.
(There is the extra T before the variant bases and the position is one base before.)

dbSNP is reporting in the same way (e.g., rs386627398 is ATAT > AAAC).

Does anyone know of a program that will phase MNVs to match what seems to be the expected nomenclature?

Thank you.
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