Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Samtools mpileup_Paired Tumoral / Germline_keep only somatic mutations

    I performed a genomic capture (Agilent technologie, SureSelect Target Enrichment System for Illumina Paired-end Sequencing) with paired tumoral and constitutional DNAs.
    I created a .bam file for each both. I used bwa for alignment and samtools to create my bam file.
    Now, I would like to call somatic mutations from these pair of samples (Tumoral vs Germline) with samtools (example of commands : samtools mpileup -DSuf ref.fa aln.bam | bcftools view -bvcgT pair - > var.bcf ). The goal is to eliminate all the commons mutations present in the two samples in order to keep only the somatic mutations.
    Anybody can help me to understand how to realize this step?
    What is the command for samtools ?
    Thank you very much for your help
    Sam64

  • #2
    did you check VarScan? It declares somatic state for each SNP/indel and provides some nice statistics by inputting the pileup files of the tumor/normal samples.

    Comment


    • #3
      Sam64, it sounds like VarScan might be better suited to your needs.

      Homepage: http://varscan.sourceforge.net

      Download: https://sourceforge.net/projects/varscan/files/

      Method Overview: http://varscan.sourceforge.net/somatic-calling.html

      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
      33 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 03-08-2024, 08:03 AM
      0 responses
      72 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 03-07-2024, 08:13 AM
      0 responses
      81 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