Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • what is DP4 in VCF (Variant Call Format) and AF1?

    Hi,
    Anyone knows what is DP4 in VCF? (I got from mpileup->bcftools view->)
    In this VCF line:
    chr1 1467416 . G C,T,X 35 . DP=105;AF1=0.5;CI95=0.5,0.5;DP4=36,33,30,5;MQ=47;PV4=0.001,3.5e-05,3.2e-21,0.0073
    I undersatnd that:
    DP=105 means Depth (or Coverage) is 105.
    then what is DP4? DP4=36,33,30,5
    I counted number of A/C/G/C , total is 105 but only about half A half C:
    (see this pileup)
    chr1 1467416 G G 62 0 49 105 .$C$C$C.CC,CCCCC.C.C.CCCC.C.C.C.CCCCCC,T..C...,.CCC.,
    .,..,Ct,...,.c,c.cc,,,,,,,,.,,,,.,,,,.,..,.,.,,.,.,,^].^].^]. D!0,2))I3+8)3F+H%44'#2I4II-III22I4II7,I0IIIIFIIIIII/II03%HI<0III2IIIIHI%I#FIII)I1III56IIIIIIIBII/I6IE7@EE




    thanks a lot!

  • #2
    There's a definition of DP4 on http://samtools.sourceforge.net/mpileup.shtml

    Comment


    • #3
      thanks, I saw the definition of DF4, but still not solving my problem:
      for example: how many C and G in this line?

      chr1 10725 . A C,G,X 34 . DP=17;AF1=1;CI95=1,1;DP4=0,0,17,0;MQ=18 PL 67,45,72,67,0,29,45,66,7
      2,67

      Comment


      • #4
        DP4 refers to the reads covering the reference forward, reference reverse, alternate forward, alternate reverse bases. Eg DP4=2,3,0,0 means 2 reads are the reference base, forward strand, 3 reference base, reverse strand, and no covering reads have an alternate at that position. The sum of DP4 will not always equal DP due to some reads being of too low quality.

        Comment


        • #5
          Originally posted by gcrdb View Post
          thanks, I saw the definition of DF4, but still not solving my problem:
          for example: how many C and G in this line?

          chr1 10725 . A C,G,X 34 . DP=17;AF1=1;CI95=1,1;DP4=0,0,17,0;MQ=18 PL 67,45,72,67,0,29,45,66,7
          2,67
          I think for that reason, you can generate the pileup without -g or -v flag and look at that loci to see how many C and Gs.

          Comment


          • #6
            Originally posted by Tally View Post
            DP4 refers to the reads covering the reference forward, reference reverse, alternate forward, alternate reverse bases. Eg DP4=2,3,0,0 means 2 reads are the reference base, forward strand, 3 reference base, reverse strand, and no covering reads have an alternate at that position. The sum of DP4 will not always equal DP due to some reads being of too low quality.
            Anyone knows exactly what constitutes "high quality" in DP4?

            Comment


            • #7
              There's no strict definition of high quality, it'll depend on the program used to call the sites (there's no guarantee that a DP4 field will even exist in any given VCF file).

              Comment


              • #8
                Originally posted by dpryan View Post
                There's no strict definition of high quality, it'll depend on the program used to call the sites (there's no guarantee that a DP4 field will even exist in any given VCF file).
                What about samtools | mpileup | bcftools in particular?
                I know mpileup has a default base quality of 13 and mapping quality of 0, but that's "raw depth" right?
                What does samtools' high-quality mean?

                Comment


                • #9
                  You'd have to go through the source code to find out, I've never seen the specifics described anywhere.

                  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, 05-24-2024, 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
                  20 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