Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • snp calling with bwa-samtools

    hi,everyone! I do wet experiment verification for my heterozygous snp found by bwa-samtools in rice genome recently,however only three of fourteen got experiment support, the rest didn't get! I have checked the reads coverage in the position of SNPs, all the indication are that they are SNPs!
    Could someone explain that?

    all the reply are appreciated!

  • #2
    1. Sequencing error
    2. Mapping error
    3. Validation error.

    Those are 3 possibilities, I'm sure there are more. You don't provide much info so it's hard to know for sure.

    Comment


    • #3
      i also meet the problem,can we have a chat? my email:[email protected] QQ:872664567

      Comment


      • #4
        Hello heiya, my experience is that using samtools with default settings will give you a high number of false positives, this could be what you are seing.

        You could try running snp-calling with the GATK using the built-in recalibration options. GATK has quite a low number of false positives. Compare the results from GATK with your existing results, and see what you get.

        Ø

        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...
          Yesterday, 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, Yesterday, 07:17 AM
        0 responses
        12 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 05-02-2024, 08:06 AM
        0 responses
        19 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 04-30-2024, 12:17 PM
        0 responses
        20 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 04-29-2024, 10:49 AM
        0 responses
        29 views
        0 likes
        Last Post seqadmin  
        Working...
        X