Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • petter
    replied
    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?

    Leave a comment:


  • Jane M
    replied
    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)

    Leave a comment:


  • petter
    replied
    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

    Leave a comment:


  • petter
    started a topic VarScan pileup2snp VarFreq calculation

    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

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