Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • count number of A,C,G,T using DP4 in VCF

    Hi,
    Not sure about DP4 format in VCF of A,C,G,T count
    chr1 90119 . T G,A,X 99 . DP=121;AF1=1;CI95=1,1;DP4=0,7,33,81;MQ=51;PV4=0.19,1,1,0.064 PL 255,208,255,255,0,255,255,255,255,255


    Which one is correct? (Total DP=121= 7+33+81 seems okay.)
    T is 7, G is 33 , A is 81 , C is 0
    T is 7, A is 33 , G is 81, C is 0
    T is 77, forward A/G is 33, reverse A/G is 81, C is 0


    How about this one?
    chr4 1808445 . C T,G,A 99 . DP=459;AF1=1;CI95=1,1;DP4=33,55,260,108;MQ=31;PV4=1.3e-08,3.1e-44,1,4.3e
    -05 PL 186,164,255,255,0,255,255,255,255,255
    I guess: C=33+55, but how many T,G,A ?? Help please.

    thanks,


    According to http://samtools.sourceforge.net/mpileup.shtml

    DP4 is:
    Number of 1) forward ref alleles; 2) reverse ref; 3) forward non-ref; 4) reverse non-ref alleles, used in variant calling. Sum can be smaller than DP because low-quality bases are not counted.
    Last edited by gcrdb; 03-23-2011, 11:32 AM.

  • #2
    Could you answer this question? I have also similar question?

    Comment


    • #3
      T is 7, forward A/G is 33, reverse A/G is 81, C is 0

      I don't think there is any way of knowing how many G's and A's from DP4, because these are both lumped under 'non-reference'. Have a look at that position in the alignment using tview to confirm this.

      If someone knows of a way to obtain this information from mpileup I would also be very interested to know, as it would be hard to call the right SNP at this location without it.

      Comment


      • #4
        Did anyone have any luck finding an answer to this?

        Thanks

        Comment


        • #5
          Did anyone have any luck finding an answer to this?

          Thanks

          Comment

          Latest Articles

          Collapse

          • 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
          • seqadmin
            Essential Discoveries and Tools in Epitranscriptomics
            by seqadmin




            The field of epigenetics has traditionally concentrated more on DNA and how changes like methylation and phosphorylation of histones impact gene expression and regulation. However, our increased understanding of RNA modifications and their importance in cellular processes has led to a rise in epitranscriptomics research. “Epitranscriptomics brings together the concepts of epigenetics and gene expression,” explained Adrien Leger, PhD, Principal Research Scientist...
            04-22-2024, 07:01 AM

          ad_right_rmr

          Collapse

          News

          Collapse

          Topics Statistics Last Post
          Started by seqadmin, 05-14-2024, 07:03 AM
          0 responses
          20 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 05-10-2024, 06:35 AM
          0 responses
          44 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 05-09-2024, 02:46 PM
          0 responses
          54 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 05-07-2024, 06:57 AM
          0 responses
          43 views
          0 likes
          Last Post seqadmin  
          Working...
          X