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Filter out reads with bad pairing (and related) properties

Category Read Filters


This filter is intended to ensure that only reads that are likely to be mapped in the right place, and therefore to be informative, will be used in analysis. The following cases will be filtered out:

  • is not paired
  • mate is unmapped
  • is duplicate
  • fails vendor quality check
  • both mate and read are in the same strand orientation

Usage example

     java -jar GenomeAnalysisTk.jar \
         -T ToolName \
         -R reference.fasta \
         -I input.bam \
         -o output.file \
         -rf MateSameStrand

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GATK version 3.6-0-g89b7209 built at 2017/02/09 12:52:48.