Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • VarScan pileup2snp VarFreq calculation

    I have a question about how VarFreq is calculated in pileup2snp.

    I’ve got these results:

    Chrom 1
    Position 260300
    Ref G
    Cons R
    Reads1 3
    Reads2 6
    VarFreq 50%
    Strands1 1
    Strands2 2
    Qual1 42
    Qual2 22
    Pvalue 0.004525
    MapQual1 1
    MapQual2 1
    Reads1Plus 3
    Reads1Minus 0
    Reads2Plus 4
    Reads2Minus 2
    VarAllele A


    Shouldn’t VarFreq be #Reads2/(#Reads1 + #Reads2)=3/(3+6)=1/3?

    and at another position I've got:

    Reads1 0
    Reads2 8
    VarFreq 80%

    What am I missing here?

    Also, when I look at the bam file in tablet there are more than 100 reads. Why only 9 reads in output from pileup2snp?

    Kind Regards
    Petter

  • #2
    snp freq calculation

    Can anyone comment or answer my question above? What is the formula for VarFreq? It has to involve some other measurements (e.g quality scores) than just read counts. Otherwise the output is slightly wrong for many of the variants.

    regards Petter

    Comment


    • #3
      I do not use the pileuptosnp command so I cannot help on your VarFreq problem.
      But concerning
      Also, when I look at the bam file in tablet there are more than 100 reads. Why only 9 reads in output from pileup2snp?
      Did you run mpileup with -A and especially -B options to generate your pileups? (you can find several topics about this issue on seqanswers)

      Comment


      • #4
        mpileup2snp

        Thanks Jane,

        The -B and -A option using mpileup helped a lot.

        Still though I can't understand how the varfreq (freq column in mpileup2snp) is calulated? Anyone who can answer this?

        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
        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