snippy
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tseemann
:scissors: :zap: Rapid haploid variant calling and core genome alignment
Hi, I am running snippy but it is providing empty .tab and .csv file which means no output. I am attaching the log file so if anyone can help me....
Hi, I had encounter a case with a SNP not detected by Snippy on a strain (call it 'toto'). After running Snippy-core (with "toto"), the resulting ".vcf" show for this...
Hi Any plans to expand snippy with support for pacbio and nanopore reads? Noticed this tutorial demonstrating the cool stuff snippy can do https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/microbial-variants/tutorial.html and came here to check it...
My code and printed output: > (base) bio-24046:~ jvanderwoude3$ snippy --outdir trial --ref PAO1.gbk --R1 CF1_LeftLower_D12_R1.fastq.gz --R2 CF1_LeftLower_D12_R2.fastq.gz > [12:13:56] This is snippy 4.6.0 > [12:13:56] Written by Torsten Seemann...
When trying to run snippy with calls to target sites of interest (in the form of a bed file), the freebayes-parallel part of the pipeline only works if the absolute...
I'm trying install Snippy on my Macbook with M1 chip. After "brew install brewsci/bio/snippy" and running snippy, it says: Can't locate Bio/SeqIO.pm in @INC (you may need to install the...
Hello, I ran snippy-multi on a set of 24 samples. According to the log output and the snps.tab file for each sample, 13 of them had a deletion at the...
[14:55:34] Need samtools --version >= 1.7 but you have 0 - please upgrade it. How to solve this problem, please?
Hi, After update snippy, I used snippy again, the error happened. the error information: ### snpEff build -c reference/snpeff.config -dataDir . -gff3 ref WARNING: All frames are zero! This seems...
