Question: Snpeff - Reports Gain Of Stop Codon As Frame_Shift In Some Cases
gravatar for John David Osborne
7.0 years ago by
John David Osborne160 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
snpeff snp • 1.0k views
ADD COMMENTlink modified 6.9 years ago by Jennifer Hillman Jackson25k • written 7.0 years ago by John David Osborne160
gravatar for Jennifer Hillman Jackson
6.9 years ago by
United States
Jennifer Hillman Jackson25k wrote:
Thanks John, Pablo, Updates are of course welcomed in the Tool Shed. Thanks for letting the Galaxy community aware that this may come up during analysis. Best, Jen Galaxy team -- Jennifer Jackson
ADD COMMENTlink written 6.9 years ago by Jennifer Hillman Jackson25k
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