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Questions tagged [snpeff]

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2 answers
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which SNP effect software, such as VEP, annovar or snpEff, allows the user to submit their own annotations in gtf format?

I have a use case where I want to annotate the variants from running Oxford Nanopore's Medaka on a very simple reference, a single sequence starting on an ATG and finishing on a stop codon (no introns)...
719016's user avatar
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2 votes
2 answers
183 views

Bacterial genomes and snpeff warnings 'WARNING_TRANSCRIPT_NO_START_CODON'

I annotated a bunch of genomes with snpeff. And although the original reads' qualities and the matches with the reference genomes were quite high, I see the above mentioned warning in almost every ...
Anti's user avatar
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1 vote
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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): ...
Anti's user avatar
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1 vote
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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 ...
art987's user avatar
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1 vote
0 answers
138 views

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 ...
Set's user avatar
  • 241
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2 answers
72 views

Questions regarding the detection of variants (SNPs and Indels) in mammal

Greetings, I’m a newbie in bioinformatics working currently on my first project regarding detection of variants (SNPs and Indels) in mammal assembly genome. I used the following method to detect ...
Mohamed Moawad's user avatar
2 votes
1 answer
403 views

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? ...
kwoo's user avatar
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