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License: GNU Affero General Public License v3.0
A tool to detect structural variant
License: GNU Affero General Public License v3.0
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,
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.
Hi!
This is not an issue but a question. We are searching for structural rearrangements between two plant genomes, the parental and a derived one.
We have attempted to use SenSV, unsuccessfully, as it defaults to using the human reference genome despite specifying the parental genome in the reference file, and providing mutant reads as fastq files.
How can we identify the differences between the two genomes? What do we need to modify in SenSV options?
Thanks a lot in advance.
Regards
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.
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