Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • UnifiedGenotyper between tumor and normal

    I have 8 tumor and normal samples (16 altogether). If I want to compare the SNP's between them (8 Tumor vs 8 Normal), should I run the UnifiedGenotyper separately twice (one run for Tumor samples and another for normal) or can I run them altogether once with 16 sample bam's. What could be the best way to analyze them?

    Thanks.

  • #2
    Are these matched normals or you have 16 individuals in all?

    Running in all together would get you an average of everything, which would be a bad idea. Unless you think that your SNP of interest would be in all tumors, even putting these together would be inadvisable.

    GATK specifically says to be REALLY careful about just running the genotyper and removing the SNPs in the normals. It might be ok if you're looking for a few interesting mutations that you can verify manually, but it's not ideal for large-scale efforts.

    The authors of GATK say that they have their own effort underway, but it's not public yet. I know of another yet-unreleased effort but I don't know of of any publicly available genotyper for tumor-normal pairs.

    Comment


    • #3
      Thank you fpepin. These are matched normals of 8 pairs. I guess I will run them individually as it is advised.

      Comment


      • #4
        Running Unified Genotyper on individual samples and identifying true somatic calls would be difficult as you may require a statistical score/probability value and variant_allele_frequency (VAF) to support the calls. I see MuTect is one you may try but the tool is still not available to public. You may also look at VarScan, SomaticSniper, Joint-SNV-mix.

        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, Yesterday, 06:37 PM
        0 responses
        8 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, Yesterday, 06:07 PM
        0 responses
        8 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