MIPVAR
MIP VARiant calling tool
... in the example input files (see sampleConfigExample.txt and runConfigExample.txt).
Run command:
java -Dsnappy.disable=true -Dlogging.config=/path-to-pipeline/MIPVAR-<version>-package/conf/logback.xml -cp "/path-to-pipeline/MIPVAR-<version>-package/lib/*" org.umcn.gen.mip.pipeline.RunMIPPipeline -sampleConfig /path-to-file/sampleConfig.txt -environment EMPTY -overridePipelineConfig /path-to-file/runConfig.txt
Output:
- Bam files per sample
- VCF
- Coverages per MIP per Sample