Questions tagged [snpeff]
The snpeff tag has no usage guidance.
4 questions with no upvoted or accepted answers
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How to use -csvStats option?
I'm trying to get CSV files from snpEff -csvStats option and got stuck. I tried the code below and only got the vcf file with no contents. How can I use -csvStats option properly?
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snpEff annotation and variant in a gene
I'm using snpEff to annotate genetic variants. However, the annotation often returns more than one annotation (see below for an example):
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What is the 4th "level" of version number for the S. cerevisiae reference genome?
yeastgenome.org has releases called R64-1-1, R64-2-1, etc, with 3 "levels" of versioning but in a few places I have seen a "fourth level". For example, Ensemble calls their hosted ...
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SnpEff not correctly annotating multiple-nucleotide polymorphisms
I have some SARS-CoV-2 sequencing data that I'm trying to annotate with SnpEff, however SnpEff doesn't appear to be recognizing multiple adjacent SNPs within the same codon and correctly calling them ...
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