Unconfigured Ad

Collapse
X
 
  • Time
  • Show
Clear All
new posts
  • dr_sson
    Junior Member
    • Jan 2012
    • 1

    #1

    Which GATK step should be multisample?

    Hi everybody,
    I am new in NGS analysis and hope not to ask something already solved (or discussed), in that case please only refer me to the right discussion.
    I am writing an analysis pipeline, based on gatk, to analyse exome data.
    My question is: which step of the gatk is better to do on multiple samples?
    I figured out the following pipeline up to the UnifiedGenotyper:
    dedupplig (single sample) ->
    RealignTargetCreator (multiple) ->
    IndelRealigner (single) ->
    BaseRecalibrator (multiple) ->
    UnifiedGenotyper (multiple)

    Is this correct?

    Thank you

Latest Articles

Collapse

  • SEQadmin2
    Multiomic Liquid Biopsy: What DNA/RNA Panels Reveal That DNA Alone Can’t
    by SEQadmin2



    Tumors contain complex mixtures of cell populations that evolve in response to treatment and host-specific factors. Tissue biopsies provide only static snapshots of a tumor’s state. But what if we could follow that evolution over time using a minimally invasive technique?

    Liquid biopsies can detect tumor-derived material circulating in the bloodstream, providing a way to study treatment response, detect emerging resistance, and discover new biomarkers. Circulating
    ...
    10-14-2026, 09:55 AM
  • SEQadmin2
    New Genomics Technologies Take Aim at Long-Standing Limits
    by SEQadmin2


    Researchers using sequencing and genomics tools often have to make trade-offs. They can choose between speed or scale, short reads or long-range information, or targeted panels or a view of the whole transcriptome. New technologies that have been released this year are built to address those tough choices.

    We asked six companies the same four questions to learn about their latest products. The new technologies bring a lot to the table, including rethinking sequencing
    ...
    09-28-2026, 10:25 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by SEQadmin2, 10-22-2026, 11:13 AM
0 responses
26 views
0 reactions
Last Post SEQadmin2  
Started by SEQadmin2, 10-22-2026, 10:48 AM
0 responses
20 views
0 reactions
Last Post SEQadmin2  
Started by SEQadmin2, 10-15-2026, 10:52 AM
0 responses
36 views
0 reactions
Last Post SEQadmin2  
Started by SEQadmin2, 10-14-2026, 05:39 AM
0 responses
43 views
0 reactions
Last Post SEQadmin2  
Working...