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A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.

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<?xml version="1.0" encoding="UTF-8"?>
<Configuration status="WARN">
  <Appenders>
    <Console name="Console" target="SYSTEM_ERR">
      <PatternLayout pattern="%d{HH:mm:ss.SSS} %-5level %logger{1} - %msg%n"/>
    </Console>
  </Appenders>
  <Loggers>
    <Root level="INFO">
      <AppenderRef ref="Console"/>
    </Root>
  </Loggers>
</Configuration>