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  • samtools mpileup and duplicate reads

    Hi,

    By default, samtools mpileup ignores reads flagged as duplicates (i.e., marked with bit flag 1024 in the BAM). Does anyone know of a way of getting samtools to include duplicates in the mpileup output without having to strip the 1024 flag from the original BAM first?

    Many thanks.

  • #2
    Looks like one way is to change the code for a "one-off" special purpose mission. Make a new copy of samtools. Keep it separate from the real samtools.

    Do this ....
    Edit bam_plp_init() function in bam_pileup.c

    bam_plp_t bam_plp_init(bam_plp_auto_f func, void *data)
    {
    bam_plp_t iter;
    iter = calloc(1, sizeof(struct __bam_plp_t));
    iter->mp = mp_init();
    iter->head = iter->tail = mp_alloc(iter->mp);
    iter->dummy = mp_alloc(iter->mp);
    iter->max_tid = iter->max_pos = -1;
    iter->flag_mask = BAM_DEF_MASK;
    iter->flag_mask &= ~BAM_FDUP; // ADD THIS LINE turn off dupe flag

    make and your ready. Just point to the right version.
    Last edited by Richard Finney; 08-23-2012, 01:21 PM.

    Comment


    • #3
      That's brilliant Richard, exactly what I needed. Will give it a go. Cheers!

      Comment

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