Questions tagged [snpeff]
The snpeff tag has no usage guidance.
7 questions
2
votes
2
answers
231
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 ...
- 153
2
votes
1
answer
417
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?
...
- 29
1
vote
0
answers
147
views
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):
...
- 153
1
vote
0
answers
30
views
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 ...
- 11
1
vote
0
answers
158
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 ...
- 241
0
votes
2
answers
352
views
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)...
- 2,364
0
votes
2
answers
77
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 ...
