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  • Phantom123
    Member
    • Mar 2012
    • 13

    #1

    Tophat Bam file question

    Do i have to do any sorting on the BAM file that Tophat generates before i convert it to a bcf/vcf file (using Samtools)?

    Thanks for your help.
  • chadn737
    Senior Member
    • Jan 2009
    • 392

    #2
    Yes, use the samtools sort to create a sorted bam file. This is then appropriate as input into mpileup.

    Comment

    • Phantom123
      Member
      • Mar 2012
      • 13

      #3
      Originally posted by Phantom123 View Post
      Do i have to do any sorting on the BAM file that Tophat generates before i convert it to a bcf/vcf file (using Samtools)?

      Thanks for your help.
      Thank you.

      Comment

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