hku-bal / sensv Goto Github PK

Hi,
thank you for this nice software! I am working with barley nanopore data and I already have bam files that I previously produced with minimap2. Since it took so much time I wonder if there is a way to use SENSV starting from bam files

Thank you

Please can you provide documentation on how to specify a config.ini file or equivalent for reference genomes other than the recommended download. The software appears hardcoded to expect chromosomes labelled as "1,2,3,4" etc.

When running on some Debian-based Linux systems, it's not possible to run samtools 1.7.

samtools: error while loading shared libraries: libcrypto.so.1.0.0: cannot open shared object file: No such file or directory

Samtools is used by SENSV, so the analysis fails.

One solution is to use samtools 1.9 or newer. Link to bioconda issue with information about this: bioconda/bioconda-recipes#13958

I got around it by overriding to use samtools=1.9 and htslib=1.9 in the step-by-step build (Dockerfile here https://github.com/fa2k/dockerfiles/blob/main/SENSV/Dockerfile)

Hi there,
I have just downloaded SenSV and am currently trying to use it to analyze some WGS data (approx 4X coverage) of two cell lines. This data was generated using the recently released Nanopore Ultra-Long DNA Sequencing Kit.
I have produced an appropriate .fastq file to input into the software, and it has managed to complete Step 0 to produce the appropriate gzipped files and index.
However, I believe the next step is not working for me. In Step 1, no bam or chain files are being generated from my fastq files, depits the step completing and giving a report of the time elapsed. This has led to an error in the following steps (Step 2 and Step 2.1). I am wondering if you could please help me figure out what is going on here, as I am very keen on using the software to confirm some potentially interesting structural variants!

Thanks very much.