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  • .dict file created by picard and by samtools

    There are 2 ways of generating .dict file for human genome.

    java -jar picard.jar CreateSequenceDictionary REFERENCE=reference.fa OUTPUT=reference.dict
    samtools faidx ref.fasta

    I found that the 2 files generated in the 2 different command have different file size.

    I need .dict file for GATK and Picard. Which one is correct one?

    Thank you very much.

  • #2
    Are you sure samtools faidx is creating a .dict file? It only creates an .fai file as I recollect.

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    • #3
      There are actually 2 ways of generating .dict files.

      Either
      Code:
      java -jar picard.jar CreateSequenceDictionary REFERENCE=reference.fa OUTPUT=reference.dict
      or
      Code:
      samtools dict reference.fa -o reference.dict
      Both commands are supposed to produce the exact same .dict file. However, due to a solved error in an older version of samtools dict, there can be subtle differences. In some contigs a few positions of the sequence were lost if they are not within the usual character set [ACTG], resulting in different sequence lengths and a different md5sum.

      So to answer your question with respect to "which one is [the] correct one?"
      Picard functions correctly, so either use picard or the updated version of samtools for making the fasta sequence dictionary.
      Last edited by dvdleest; 08-24-2018, 01:11 AM.

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