MpileupToVcf

Introduction

This tool enables a user to extract a VCF file out a mpileup file generated from the BAM file. The tool can also stream through STDin and STDout so that the mpileup file is not stored on disk. Mpileup files tend to be very large since they describe each covered base position in the genome on a per read basis, so usually one does not want to safe these files.


Example

To start the tool:

java -jar Biopet-0.2.0.jar tool mpileupToVcf

To open the help:

java -jar Biopet-0.2.0.jar tool mpileupToVcf -h
Usage: MpileupToVcf [options]

  -l <value> | --log_level <value>
        Log level
  -h | --help
        Print usage
  -v | --version
        Print version
  -I <file> | --input <file>
        input, default is stdin
  -o <file> | --output <file>
        out is a required file property
  -s <value> | --sample <value>

  --minDP <value>

  --minAP <value>

  --homoFraction <value>

  --ploidy <value>