snippy
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tseemann
:scissors: :zap: Rapid haploid variant calling and core genome alignment
This file check should have a space between the `!` and `-f` otherwise it breaks in `Nextflow` where the `bed` file is symlinked ```bash err("Can't read --bed $bed") if $bed...
It should work by adding a space, tested successfully.
I am trying to run snippy, but i get the following: (base) sfb619@SUND35882 snippy % snippy --cpus 4 --outdir mysnips --ref 26B3_contigs.fsa --R1 AL8_S42_L001_R1_001.fastq.gz --R2 AL8_S42_L001_R2_001.fastq.gz --ram 3 [21:37:19] This...
Is there a way to remove SnpEff filters on the output of the vcf file. I want to include the non-coding regions? -- ##SnpEffCmd="SnpEff -noStats -no-downstream -no-upstream -no-utr ref snps.filt.vcf...
Installed snippy in conda environment in ubuntu 20.04 LTS. Following message was obtained. Assistance will be greatly appreciated. 
Hi, Please give us a better way to give you credit when we use your tools. A DOI would be nice (ex. zenodo).
$ snippy Can't locate Bio/SeqIO.pm in @INC (you may need to install the Bio::SeqIO module) (@INC contains: /home/taobilin/miniconda3/bin/../perl5 /home/taobilin/miniconda3/lib/site_perl/5.26.2/x86_64-linux-thread-multi /home/taobilin/miniconda3/lib/site_perl/5.26.2 /home/taobilin/miniconda3/lib/5.26.2/x86_64-linux-thread-multi /home/taobilin/miniconda3/lib/5.26.2 .) at /home/taobilin/miniconda3/bin/snippy line 15. BEGIN failed--compilation aborted...
I know this has been a issue previously but it has poped up again on the conda install of version 4.6. Is there a stable version that curently works through...
Is it possible to call variants for 3 samples against Reference genome 1 and then align a reference genome 2 against reference genome 1, and then finally generate 1 tree...
Hi, I am testing snippy with one bam file and everything runs ok till the last step " bcftools consensus --sample outdir -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz". After I get...
