vcf v4.2 consequences of missense snps
It appears that SIFT cannot deal with vcf version 4.2 files. I am dealing with a plant genome. What other options (tools) do I have for finding the consequences of missense snps?
vcf
plant
missense
snps
sift
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AFAIK
SIFTis just the name of the algorithm. Which program do you try to use?