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A Java application to analyse Molecular Inversion Probe sequencing data within short time.
Running the pipeline requires previous installation of three general tools: BWA, GATK and Bedtools.
Input:
For running the pipeline you need to specify 3 arguments. An example of the command is given below. The two input files are essential to specify the sample and run configuration. The environment argument should always be set to EMPTY. A brief description of other required files can be found 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
Features
- Mapping the reads with BWA
- Multi-sample calling from GATK
- Supports different sequence platforms (NextSeq, HiSeq, MiSeq and IonTorrent)
- Supports smMIP data with an option to remove duplicated reads
- Handling smMIPs with one or two random tags
- Coverages per MIP per sample (Average between forward and reverse read)
- Handling of variable MIP target lengths
- MIP arm removing and overlap trimming between forward and reverse read