nanosv
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mroosmalen
SV caller for nanopore data
Hi For reasons that escapes me, the current pipeline that uses minimap2 to align during guppy basecalling seems to emit an AL tag instead of the SM tag when producing...
Hi, Is it normal that it is almost 2 days stuck on "Busy with printing to vcf..."?
Hello, I'm trying to benchmark NIST002 vcf files produced by NanoSV against the GIAB NIST002 SV truth set, but not any variant is classfied as true positive. Here is the...
## Hi, First of all, thank you for making the tools available. I tried to call SV on some nanopore alignment, and use a powerful instance with 72cpus and define...
The usual mode works well for me (w/o phasing). Apart from the usual inputs and settings. I set `phasing_on = True` in my config file, and add `-f snp.vcf` in...
I know I'm somewhat screaming into the void of an unmaintained package here, but for posterity: nanosv requires sambamba to run. This is not specified as a dependency in the...
Hi, I got an issue: `conda install -c bioconda nanosv ` ``` Collecting package metadata (current_repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Solving environment:...
Hi Mark, I got the following error message during NanoSV (version 1.2.4) run on centos7 environment. command I was using: `NanoSV test.bam -b Homo_sapiens.GRCh38.100.remapped.bed -o . -s sambamba_v0.5.5` error message...
Hi, I am working on human genome but bumped into the same issue of bed files not being compatible with the bam file as many others. From previous posts I...
