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  • bam file statistics

    Hi:
    Is there any program to obtain detailed bam file statistics in addition to common stats such as:
    # of total reads mapped.
    # of total reads where read mapped and mate unmapped.
    thanks
    Adrian

  • #2
    check out samtools with flagstat option

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    • #3
      Have a look at Picard tools

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      • #4
        You can get some of that from 'samtools idxstats' (very fast - gets the counts from the BAM index file, *.bai), but not information about paired reads.

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