Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • deletion '*' has quality score in pileup?

    I know that asterisks '*' in read bases column represent deletions as place holders in pileup format. But in my data, deletion '*' seems to has base quality score. why deleted bases have base qualities?

    In this example, there are 6 bases and 1 deletion at the site 25, and the number of base qualities is 7. Can I simply ignore the base quality 'a' corresponding to the deleted base?

    chr1 24 g 7 ,..,-1t.,, ``a]bb\
    chr1 25 t 7 ,..*.,, b[baaa`
    chr1 26 t 7 ,..,.,, a_baa]_

    Thanks in advance.

    FYI:

    I constructed pileup file by using the following command

    $ ./samtools-0.1.7a/samtools pileup -f reference.fa <in.bam> > <out.pileup>

  • #2
    The base quality is also a place holder just as the * in the reads column.

    I found similar occurrences in my data (created with samtools pileup -vcf), e.g.

    chr14 65392038 T A 0 0 0 1 * W

    Note that the weird consensus A must result from a floating underflow in the MAQ SNP calling model (http://sourceforge.net/apps/mediawik...?title=SAM_FAQ). Although the FAQ answer says that this only happens in repetitive regions, the reference T is upper case and I just checked again in the UCSC Genome Browser for hg19 that there is no repeat. So I guess the reason is that there is only one read.

    Comment


    • #3
      Originally posted by luxmare View Post
      I know that asterisks '*' in read bases column represent deletions as place holders in pileup format. But in my data, deletion '*' seems to has base quality score. why deleted bases have base qualities?
      I don't know how samtools handles this particularly, but the IDEA of giving a deletion a "quality score" is good. A quality score is essentially just a logarithm of a "probability of error" or "probability that this is wrong". So you can interpret it as a statistical confidence of the deletion being real.

      Comment


      • #4
        Hi Torst,
        Thank you for your reply. I agree with you. Quality scores of deletions is informative. But if the pileup format (made by BWA->SAMtools) was designed based on the IDEA you said, inserted bases should have base quality scores. Actually, however, inserted bases don't have qualities as below. I'm confusing...


        chr3 7759 C 4 ..,, SO]^
        chr3 7760 C 4 .+1G.,, \\\[ <-- 4 ref-type bases and 1 insertion, but only 4 qualities
        chr3 7761 G 4 ..,, GT[a

        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,”...
          05-24-2024, 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, Today, 01:32 PM
        0 responses
        4 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 05-24-2024, 07:15 AM
        0 responses
        198 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 05-23-2024, 10:28 AM
        0 responses
        220 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 05-23-2024, 07:35 AM
        0 responses
        229 views
        0 likes
        Last Post seqadmin  
        Working...
        X