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Filter out reads with wonky CIGAR strings

Category Read Filters


This read filter will filter out the following cases:

  • different length and cigar length
  • Hard/Soft clips in the middle of the cigar
  • starting with deletions (with or without preceding clips)
  • ending in deletions (with or without follow-up clips)
  • fully hard or soft clipped
  • consecutive indels in the cigar (II, DD, ID or DI)

Usage example

Enable the bad cigar filter

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

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