Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • mpileup: specified region truncated.

    Hello gentlepeople,

    I am using the samtools 'mpileup' program.
    I wish to generate a pileup file for a specific region.
    I have several separate .bam input files that I am generating the pileups for.
    Unfortunately, mpileup truncates the region and I only get data for the first part of the region.
    I have ran the same command on different .bam files and get different results.

    When I command:

    samtools mpileup -f 'hg19.fa' -r chr6:27114408-27115845 'experiment01.bam' > out_PILEUP2.pile
    [mpileup] 1 samples in 1 input files
    <mpileup> Set max per-file depth to 8000

    I get a file with 746 lines.
    I am expecting 1438 lines because that is the size of the interval I have specified with the '-r' flag
    If I use mpileup with the same region but with a different .bam file I get a different size file.

    samtools mpileup -f 'hg19.fa' -r chr6:27114408-27115845 'experiment02.bam' > out_PILEUP3.pile
    [mpileup] 1 samples in 1 input files
    <mpileup> Set max per-file depth to 8000

    I get a file with 623 lines.
    Again, I am expecting 1438 lines because that is the size of the interval I have specified with the '-r' flag.

    The first line in both files is for chr6:27114408, as expected.
    BUT, the files are truncated at different positions.
    With experiment01.bam the final line of the pileup file is chr6:27115577.
    With experiment02.bam the final line of the pileup file is chr6:27115344.

    This must have something to do with the .bam file.
    Can someone tell me which parameter needs to be adjusted?
    I have consulted the manual but I could not identify anything that sounded applicable.

    Thanks for you time,
    Lionel (Lee) Brooks 3rd
    Dartmouth Genetics Grad Student

  • #2
    The simplest answer is that you just don't have any reads across part of your region.

    Try getting the .sam file for the same region +- 500 bases, or try looking at the whole .bam in IGV. You can zoom in on your region.

    Comment


    • #3
      Yeah, mpileup doesn't generate lines for regions it has no reads on. If you need to work out whole-region coverage, then you should be looking at the column that gives the base number. For covered regions, this will increase by 1 per line (assuming no inserts), but will jump multiple bases when there are no reads.

      Comment


      • #4
        whoops, should have checked that...thanks!

        Comment

        Latest Articles

        Collapse

        • seqadmin
          Latest Developments in Precision Medicine
          by seqadmin



          Technological advances have led to drastic improvements in the field of precision medicine, enabling more personalized approaches to treatment. This article explores four leading groups that are overcoming many of the challenges of genomic profiling and precision medicine through their innovative platforms and technologies.

          Somatic Genomics
          “We have such a tremendous amount of genetic diversity that exists within each of us, and not just between us as individuals,”...
          Yesterday, 01:16 PM
        • seqadmin
          Recent Advances in Sequencing Analysis Tools
          by seqadmin


          The sequencing world is rapidly changing due to declining costs, enhanced accuracies, and the advent of newer, cutting-edge instruments. Equally important to these developments are improvements in sequencing analysis, a process that converts vast amounts of raw data into a comprehensible and meaningful form. This complex task requires expertise and the right analysis tools. In this article, we highlight the progress and innovation in sequencing analysis by reviewing several of the...
          05-06-2024, 07:48 AM

        ad_right_rmr

        Collapse

        News

        Collapse

        Topics Statistics Last Post
        Started by seqadmin, Yesterday, 07:15 AM
        0 responses
        13 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 05-23-2024, 10:28 AM
        0 responses
        17 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 05-23-2024, 07:35 AM
        0 responses
        19 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 05-22-2024, 02:06 PM
        0 responses
        10 views
        0 likes
        Last Post seqadmin  
        Working...
        X