Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Less SNVs with larger interval file - MuTect

    Hi,
    I've used MuTect to call variants on .bam files (standard procedure for exome seq, tumor vs normal) using two different interval files (both from Illumina website): Nextera Exome Capture and Nextera Exome Capture Expanded. These intervals correspond to different kit versions, with expanded kit spanning about twice more targeted regions (~60Mb vs ~30Mb). The libraries has been created using Expanded kit.
    To my surprise, providing with 30Mb interval file resulted in 674 SNVs; same bam/MuTect parameters with 60Mb interval file gave 545 SNVs (here I refer to KEEP SNVs; total SNVs are also decreased when larger interval file is used).
    I am going to study how these sets overlap, but anyway I cannot understand this. Even if no more additional mutations is present in regions from larger interval file as compared to smaller one, still reduction to over 100 SNV (129) seems too large. I just cant trust my data analysis when I see such things.
    Did anybody experienced similar before?
    Thanks,
    Artem

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
10 views
0 likes
Last Post seqadmin  
Started by seqadmin, Yesterday, 06:07 PM
0 responses
9 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-22-2024, 10:03 AM
0 responses
51 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-21-2024, 07:32 AM
0 responses
67 views
0 likes
Last Post seqadmin  
Working...
X