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  • samtools failed to index if sorted by name

    Hi, I am relatively new to this field, please bear with me if my question is naive.

    It works if -n is dropped. What should I do if I need the index file of sorted by name bam file for downstream analysis? The commands I used:

    samtools sort -n aln.bam aln.sorted
    samtools index aln.sorted.bam

  • #2
    See this thread for additional information: http://seqanswers.com/forums/showthread.php?t=16375

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    • #3
      Thanks GenoMax! This is very helpful! Appreciate!

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