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

Project Activity

See All Activity >

Categories

Follow MIPVAR

MIPVAR Web Site

Other Useful Business Software

Focus on your Business with an integrated Business Cloud Focus on your Business with an integrated Business Cloud Icon
Focus on your Business with an integrated Business Cloud Icon

Reliable & Secure Business Phone Systems

  • No contracts, no cancellation fees, over 40 features
  • 99.999% financially backed uptime SLA
  • Free, expert support, certified by J.D. Power

Rate This Project

Login To Rate This Project

User Reviews

Be the first to post a review of MIPVAR!

Additional Project Details

Registered

2016-04-12