Run Manta to get structural variants

Manta ^[1]

Manta calls structural variants (SVs) and indels from mapped paired-end sequencing reads.

Installation

Follow the instruction for different operating system ^[2]

Usage

Somatic configuration examples Tumor Normal Analysis -- Example Configuration:

${MANTA_INSTALL_PATH}/bin/configManta.py \
--normalBam HCC1187BL.cram \
--tumorBam HCC1187C.cram \
--referenceFasta hg19.fa \
--runDir ${MANTA_ANALYSIS_PATH}

${MANTA_ANALYSIS_PATH}/runWorkflow.py

Output

├── Sample_name
│   ├── results
│   │   ├── evidence
│   │   ├── stats
│   │   ├── variants
│   │   │   ├──candidateSmallIndels.vcf.gz
│   │   │   ├──candidateSV.vcf.gz
│   │   │   ├──diploidSV.vcf.gz
│   │   │   ├──somaticSV.vcf.gz
│   ├── runWorkflow.py.config.pickle
│   ├── workflow.error.log.txt
│   ├── workflow.exitcode.txt
│   ├── workflow.warning.log.txt

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1. https://github.com/Illumina/manta ↩︎

2. https://github.com/Illumina/manta/blob/master/docs/userGuide/installation.md#linux ↩︎