snippy
snippy copied to clipboard
tseemann
:scissors: :zap: Rapid haploid variant calling and core genome alignment
I have a question not an issue about Snippy. Could we extract the genes that are affected by snp/indels from the query genomes?
Hi! it would be great to have an option to set the zero coverage symbol at execution to easily distinguish between uncovered regions and genuine deletions. Of course, we can...
I just installed a fresh version of snippy on linux with conda, I get the following error in snps.log when I'm calling with reads: ``` ### bcftools view --include 'FMT/GT="1/1"...
Hi, I have tried generating tab file by pasting all the filenames and paths in excel and later converted that CSV file using this command. `sed -e 's/,/\t/g' input.csv >...
Ie. does Snippy consider non-annotated, non-coding regions at all? I assume they don't appear in the .gbk reference and are thus not considered, correct? Thanks for clarifying this, Kind regards
Hi, I am following this tutorial to produce phylogenetic trees: https://aschuerch.github.io/MolecularEpidemiology_AnalysisWGS/09-SNPphylo/index.html I used the fastq files of my bacterial isolates using the fast of the original one as a reference...
Can we use Snippy for phylogenetic tree construction for COVID-19 from Fastq reads. If not, Can you suggest some tool to work with fastq reads
Hello, I am using snippy 4.6.0. I got a deletion described as 28 base pairs. However, when I did the alignment of the reference with the file snps.consensus.fa, the sequences...
Checking some samples in IGV, I noticed several genotypes where snippy-core called the REF allele, even though none of the aligned reads were REF. Inspecting more closely, this happens because...
the script "snippy-multi" is not a effctive order, and I make a folder contained the 100 genomic contigs as input.tab, is it right?
