Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • mpileup -B option

    Hi there
    I used mpileup with the -B option to predict variations. To evaluate our pipeline, the same analysis has been done by an other lab and results have been validated in wet lab.
    we share true positive prediction... good. But also we missed A LOT of true positive. I checked without the -B option and they are found. A lot of reads were not considered by using -B ... and it was wrong to do that
    I'm wondering if you know which parameters I can play with to be less stringent.
    Thanks for your time

  • #2
    That's my experience too. Real, sanger validated SNPs will turn up with -B is selected, but won't be called otherwise.

    Here's the result running

    ../../../../samtools/1.14/samtools mpileup -f ../1/genome6.fa region.bam > mpileup_noB.txt
    598255 C 136 t,ttttttT.tttt.ttTTT.ntnn.t.t.,t.,,.TTTTtT..Tttt,T.tTtttTT.tttttttttTT.t,ttttt,t.T...tTTTtTTtttt.tT.TtTTTT.TTT.Tt,.ttttt,TtTTTt,ttttTTT^Ft !U!!!!!!!g!!>!B!!!%!BE!BDf!h!ag!hhYh!!!!!!h]*!!!f0g!%!!!!!Z!!!!!!!!!!>g!c!$!!!h!f!hhh!!!!!,!!!!!h!!g!%!!!$h!!!h!$BS!!>!!g!!!!!!b#!!!!!!!

    ../../../../samtools/1.14/samtools mpileup -Bf ../1/genome6.fa region.bam > mpileup_B.txt

    598255 C 136 t,ttttttT.tttt.ttTTT.ntnn.t.t.,t.,,.TTTTtT..Tttt,T.tTtttTT.tttttttttTT.t,ttttt,t.T...tTTTtTTtttt.tT.TtTTTT.TTT.Tt,.ttttt,TtTTTt,ttttTTT^Ft ggThghghfghgBfBghh^dBEhBDfdhhagghhYhfgfdhgh]WffffPgf]fhggcZdfghhffhhgBghcg_hhchgfghhhefghgThPhafhfdgh^a`hZhfghhe_BS`gBghghghhhhg]hdhgfgf

    the -B has for some reason destroyed the quality scores of the letters in this area, and the vcf is empty in this region. When I make it starting with -B, then that SNP pops up.

    It's mixed, but the sanger was plain as day.

    Comment

    Latest Articles

    Collapse

    • seqadmin
      Strategies for Sequencing Challenging Samples
      by seqadmin


      Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
      03-22-2024, 06:39 AM
    • seqadmin
      Techniques and Challenges in Conservation Genomics
      by seqadmin



      The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

      Avian Conservation
      Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
      03-08-2024, 10:41 AM

    ad_right_rmr

    Collapse

    News

    Collapse

    Topics Statistics Last Post
    Started by seqadmin, Today, 06:37 PM
    0 responses
    6 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, Today, 06:07 PM
    0 responses
    6 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 03-22-2024, 10:03 AM
    0 responses
    49 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 03-21-2024, 07:32 AM
    0 responses
    66 views
    0 likes
    Last Post seqadmin  
    Working...
    X