How good is SNPeff anotation? does it just output "synonymous" or "nonsynonymous" only? or can it give you a full cDNA , HGVS formatted output? eg. c.1279G>T , and p.T289F ? And if it does do that, can it handle splice mutations in the HGVS format? (eg. c.196-1G>T or c.241+2A>T ) ?
Anyone know if the ensembl variant annotator API can do that?
I know ANNOVAR can output this in HGVS format.
These are the formats used in the literature, and not having the variants reported in this format makes comparison and integration with other data sets a bit clumsy.
Anyone know if the ensembl variant annotator API can do that?
I know ANNOVAR can output this in HGVS format.
These are the formats used in the literature, and not having the variants reported in this format makes comparison and integration with other data sets a bit clumsy.
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