ClinSV
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KCCG
Robust detection of clinically relevant structural and copy number variation from whole genome sequencing data
Hello, FIY runnig master branch of ClinSV display version 0.9 and date fromthe past. see: ``` clinsv -h ### This script runs ClinSV on a single node ### Version: 0.9...
Hi all, I run into issue of xml file generation with wrong reference genome. When I submit the run using command: input_path=/input_dir/ refdata_path=$PWD/clinsv/refdata-b38 project_folder=$PWD/449_WT docker run -v $refdata_path:/app/ref-data -v $project_folder:/app/project_folder...
Hello, playing with version 1.1.dev I nioticed that commit https://github.com/KCCG/ClinSV/commit/c20c21a3c604c7b484daf6b66223c994dfbc458e seems to have wrong perl shell syntax escaping seems to me that [line ](https://github.com/KCCG/ClinSV/blob/dev-ClinSV-v1.1/clinsv#L476) should be. `print OUT "[ -z...
Hello using ClinSV-1.0.0 we noticed some potential problem when ClinSV is run through the use of taskset, batch system like slurm, etc... clinsv have some harcoded number of process for...
Hello, I noticed in the install from sources documentation, more specifically in install python section. https://github.com/KCCG/ClinSV/blob/master/INSTALL_b38.md#install-python python2 is required clinsv uses python2 for lumpy calls lumpy requires `numpy pysam` python3...
Hi all, I am running test dataset based on refdata-b38 and got the following error: "error exist status != 0 (256), please check /app/project_folder/SVs/FR05812606/cnvnator/sh/cnvnator.caller.FR05812606.e for more information". The error file...
Hello ClinSV team! Great software, we include it regular in our new workflows! We would like to re-analyse old data, but the alignments are compressed in CRAM files. We are...
Hi folks, We want to use clinSV with hg38 bams and we found that we should use the container for this reference. We don't have permission to run docker in...
Hello, I have a little problem with ClinSV. Both versions on dockers v0.9 and v1.0, after some time from the start of processing, the analysis stops with the following message:...
u said that "PAF1KG" is population variant in 1000 Genome, so why i get the value "-1"? And i hvae get some break ends (BND) result, PAFG and PAF1KG =...
