Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • samtools indels

    Hi everyone,
    I have a problem calling indels with samtools. Up to now, I called variants with the following command:
    samtools pileup -vcf ref.fasta mapping.bam > raw_variants.var
    and created the pileup file with:
    samtools pileup -cf ref.fasta mapping.bam > mapping.pileup
    After that I added the filter steps. But for my last samples I didn't receive any indels (just SNPs). In the mapping I can see indels, but neither in the pileup-file nor in the variance-files are indels. Are there any parameter to include/exclude indels? Or do I have to do anything different for Solid-reads mapped with Bioscope in comparision to Illumina-reads?

    Thanks for your help!

  • #2
    Have you thought about updating to the newer version of SAMtools that uses mpileup instead of pileup?

    Comment


    • #3
      I tried with mpileup as well, but also in that file I can't see the indels

      Comment


      • #4
        Try these commands:

        samtools-0.1.18/samtools mpileup -AB -ugf <reference_sequence> <aligned_file> | samtools-0.1.18/bcftools/bcftools view -bvcg -> <intermediate_file>

        samtools-0.1.18/bcftools/bcftools view -e <intermediate_file> | samtools-0.1.18/bcftools/vcfutils.pl varFilter -D99999 > <variants.txt>

        Comment

        Latest Articles

        Collapse

        • 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
        • seqadmin
          The Impact of AI in Genomic Medicine
          by seqadmin



          Artificial intelligence (AI) has evolved from a futuristic vision to a mainstream technology, highlighted by the introduction of tools like OpenAI's ChatGPT and Google's Gemini. In recent years, AI has become increasingly integrated into the field of genomics. This integration has enabled new scientific discoveries while simultaneously raising important ethical questions1. Interviews with two researchers at the center of this intersection provide insightful perspectives into...
          02-26-2024, 02:07 PM

        ad_right_rmr

        Collapse

        News

        Collapse

        Topics Statistics Last Post
        Started by seqadmin, 03-14-2024, 06:13 AM
        0 responses
        32 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 03-08-2024, 08:03 AM
        0 responses
        71 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 03-07-2024, 08:13 AM
        0 responses
        80 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 03-06-2024, 09:51 AM
        0 responses
        68 views
        0 likes
        Last Post seqadmin  
        Working...
        X