ClinSV
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KCCG
Robust detection of clinically relevant structural and copy number variation from whole genome sequencing data
When I run ClinSV, errors has happened. The command is : docker run -v /project/ShareJH/Clinsv/clinsv/:/app/ref-data -v /project/JX1/04.sv/WGS1/:/app/project_folder -v /project/JX1/01.alignment/WGS1/:/app/input --entrypoint "perl" mrbradley2/clinsv:v1.1-dev /app/clinsv/bin/clinsv -r all -p /app/project_folder/ -i "/app/input/*.bam" -ref...
IGV hg38 fix
Dear all, I fixed IGV hg38 issue, the solution is not very clean, since I did not rewrite the code, but simply replaced b37 with hg38 and the corresponding tracks....
Hello, We run version 1.1 on a bam and all steps completed without errors. However, the coverage by chromosome view in the QC_report.pdf showed 24 lines of "## Warning: NAs...
I found two mistakes in README for the usage of clinsv1.0 part: 1. docker image mrbradley2/clinsv:v1.0.1 does not exist in DockerHub, we can choose to pull v1.0; 2. the following...
### Description Implementation of a few features that will make ClinSV more robust and efficient. ### Features to be implemented: - [x] Currently unable to switch between hs37d5 and grch38...
Thanks to the authors for your hard working on this app!!! but there is lot of errors before I can use it with singularity. I spent several days on setting...
Note sure what the error status means. I tried running the default test bam files refdata_path=/home/mai/Desktop/svclin/clinsv input_path=/home/mai/Desktop/svclin/bam_files project_folder=/home/mai/Desktop/svclin/test_run2 docker run -v $refdata_path:/app/ref-data \ -v $project_folder:/app/project_folder \ -v $input_path:/app/input \ --entrypoint...
Hello, I am running a sample, which is mapped against reference hs37d5, and I got this issue at lumpy.depth.joined.sh. The error log is shown below. Possible issues: 1) I used...
Hello running master branch of ClinSV I noticed that when project dir is given as a relative path it fails with followning error ``` rpm_maker://tmp > clinsv -i /opt/gensoft/tests/datas/ClinSV/NA12878_B37.bam -ref...
