snippy
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tseemann
:scissors: :zap: Rapid haploid variant calling and core genome alignment
When i try to use snippy outside the installed PATH, i receive this message: Can't locate Snippy/Version.pm in @INC (you may need to install the Snippy::Version module) (@INC contains: /usr/local/bin/../perl5...
Hello all, can someone tell me more about the filters which snippy/freebayes use please? We have to do a SNP call without utilize SNPs in these regions: repetitive sequences and...
This PR adds the necessary files to: 1. Create a docker container 1. Create a Gitpod workspace I was trying to add a new feature to snippy, and got caught...
Hi Torsten, My snippy analysis progresses well creating the expected output files using $sample as prefix, but errors when the BCFtools 'consensus' command is run, as the read group specified...
Hi, I am interested in exploring soft-clipped reads from some bam files I produced earlier using snippy, as a mean to identify insertion sequences. However, I'm not sure I can...
Hi, When I tested snippy, it showed this warning and exited, > Need samtools --version >= 1.7 but you have 1.11 - please upgrade it But the latest version of...
hi: when I use snippy now , I only can get the result of snps.raw.vcf, The result of snps.filt.vcf shows only the table's title.The snps.log is as follows: ### echo...
Hi, i have used snippy 4.6.0 for calling snps from the targeted region (bed file format). Some of the snps at pos 18100, 19067, 19067 were reported multiple times in...
I want to calculate nucleotide diversity using vcftools based on vcf output as bellow without success: vcftools --vcf snps.vcf --window-pi 1000 --window-pi-step 200 --out pi-out the out pt is empty...
I'm getting the could not run snp-sites error even though like others who have had this issue (e.g. #326) I don't have the warning that I have no SNPs. However,...
