snippy
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tseemann
:scissors: :zap: Rapid haploid variant calling and core genome alignment
when i train snippy using the data offered by author, snippy --outdir mut1 --ref example.gbk --ctgs example.fna I have the following problem: Error: A JNI error has occurred, please check...
I have a simple header reading error from markdup that caused my snippy to fail... I've pasted the log file below. ```### echo snippy 4.6.0 ### cd /lustre06/project/6000186/congxu/snippy/A.rubrum ### /home/congxu/0_def-barrett_project_congxu/snippy/bin/snippy...
how to compare mutations between two matched samples? For example: If you want to identify SNPs in one sample relative to another sample (for example, if you sequenced your lab...
I am running snippy using following command. However, it shows the following error.. snippy --cpus 8 --outdir variants --ref reference.gbk --R1 trimmed_S_010_R1.fastq.gz --R2 trimmed_S_010_R2.fastq.gz ### snpEff build -c reference/snpeff.config -dataDir...
Hi, I've tried uninstalling and installing snippy again, bur I'm still having the same issues. The output files aren't complete and I get this error message (see screenshot). Can anyone...
Hello all, I am trying to do vcf through snippy, but I got some errors. I have attached the log file, please help me!!! [snps.log](https://github.com/tseemann/snippy/files/8355048/snps.log) [Screenshot from 2022-03-26 14-27-51](https://user-images.githubusercontent.com/92774704/160232658-7da7431d-ab24-4da1-9cea-b304e75816e7.png)
Hi, I am working to identify hqSNPs using snippy. I used Mummer for masking the repeats in the reference genome. I am trying to understand how to use the output...
my command: ```snippy --outdir test/mysnps --ref test/REF_GCF_904425475.1_MG1655_genomic\(1\).fna --ctgs test/11657_5\#1.fa"``` ### freebayes-parallel reference/ref.txt 8 -p 2 -P 0 -C 2 -F 0.05 --min-coverage 10 --min-repeat-entropy 1.0 -q 13 -m 60 --strict-vcf...
Hello, I ran 21 isolates of complete genome (each one >1.5Mb) through snippy and then called "snippy-core" with the "snippy-multi" command, and it seemed work and no given error message....
Hello, I was wondering if there is an easy way to generate a genotype by isolate table for subsequent dnds calculation. I previously used the core.tab file from snippy-core but...
