Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Is mpileup limited in the number of samples?

    I have been using mpileup with two to six samples for a while, with good results. Today I tried a run with 20 input bam files, and a small percentage of my output lines are truncated. I haven't been able to find a reference to this on the web; my apologies if it has been discussed before.

    My use of mpileup is about as simple as can be; I'm just getting the pileups, not doing any calling:
    samtools mpileup -f <reference> <bam-list>

    With 20 input files, I expect 63 tab-separated fields per line. In a small percentage of lines, I'm getting 61 fields. When the line is short, it always has 61 fields. In a subset of my data, the total mpileup output is 26,633 lines; of those, 23 are truncated.

    I have run mpileup multiple times on the full set of the data and the output files are identical.

    If this is not a known problem and my subset bams would be helpful, I can point lh3 at them.

    Thanks for any pointers.
    -Al

  • #2
    I never tried it with that many, but I think the place to start is to believe your data. Did you check to see that in those particular areas, that every single sample has at least one read? Because if a sample has no read there, displaying nothing would seem to be what mpileup would do.

    Comment


    • #3
      These data are very "thin"; there are many locations that have no reads. However, the mpileup format handles that gracefully, reporting the triple "0\t*\t*" (\t represents a tab character) for any location that is not covered in a sample. So I don't think that these short/truncated lines are caused by the last sample not having a read there. These lines have the 0, but not the following two asterisks and their separating tabs.

      Comment


      • #4
        samtools mpileup truncated output

        Originally posted by asimons View Post
        These data are very "thin"; there are many locations that have no reads. However, the mpileup format handles that gracefully, reporting the triple "0\t*\t*" (\t represents a tab character) for any location that is not covered in a sample. So I don't think that these short/truncated lines are caused by the last sample not having a read there. These lines have the 0, but not the following two asterisks and their separating tabs.
        Has this been resolved, I am having the same problem with no asterisks after 0 with multiple sample mpileup

        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
        12 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 05-23-2024, 10:28 AM
        0 responses
        15 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 05-23-2024, 07:35 AM
        0 responses
        16 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 05-22-2024, 02:06 PM
        0 responses
        9 views
        0 likes
        Last Post seqadmin  
        Working...
        X