Question: Snpeff - Reports Gain Of Stop Codon As Frame_Shift In Some Cases
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John David Osborne • 160 wrote:
Hi Pablo,
Correct me if I am wrong, but I believe that SNPEff doesn't check the
inserted sequence when computing the effect of an insertion?
For instance an insertion of TTTA will be reported as a frameshift
mutation. In the majority of cases this is fine, however if the
current reading frame from the ORF annotation is the negative strand
and the correct frame is selected the new codon will be:
TAA T
The TAA is actually a stop codon, so the real effect of this insert
should be insertion of a STOP CODON, not a frame shift in this
instance. This is minor I know, but I though to report and make people
aware.
I am using version 2.02 of SNPEff, but I don't see this fix reported
up to 2.04.
-John
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modified 6.9 years ago
by
Jennifer Hillman Jackson ♦ 25k
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written
7.0 years ago by
John David Osborne • 160
