Unconfigured Ad

Collapse
X
Collapse
 
  • Page of 1
  • Time
  • Show
Clear All
new posts
Previous template Next
  • swNGS
    Member
    • Nov 2011
    • 83
    #1

    ? --doNotWriteOriginalQuals equivalent command in GATK 2.x ?

    In GATK 1.x there was an option to discard the original quality scores for a recalibrated bam using the switch:
    --doNotWriteOriginalQuals
    I think during TableRecalibration

    Is there an equivalent in GATK v 2.x since as far as I can see t here is no option in PrintReads after BaseRecalibrator to discard original quality scores in favour of recalibrated quality scores.
    My intention is to keep the file sizes down as much as possible

    Thanks
    Tags: gatk baserecalibration
    Previous template Next

    Latest Articles

    Collapse
    • SEQadmin2
      Beyond CRISPR/Cas9: Understand, Choose, and Use the Right Genome Editing Tool
      by SEQadmin2



      CRISPR/Cas9 sparked the gene editing revolution for both research and therapeutics.1 But this system still showed severe issues that limited its applications. The most prominent were the heavy reliance on PAM sequences, delivery limitations, double-stranded breaks that prompt unintended edits and cell death, and editing inefficiency (both in targeting and in knock-in reliability).

      Despite this, “CRISPR helped turn genome editing from a specialized technique into      ...
      Yesterday, 11:01 AM
    • SEQadmin2
      Proteomic Platforms: How to Choose the Right Analytical Strategy to Improve Detection and Clinical Applications
      by SEQadmin2


      Proteomics platforms are evolving rapidly, with advances in mass spectrometry and affinity-based approaches expanding what researchers can detect and at what scale. As the field moves toward deeper proteome coverage and clinical applications, scientists face an increasingly complex landscape of tools. This article will explore how researchers are navigating these choices to find the right platform for their work.

      The systematic characterization of the human proteome has      ...
      07-20-2026, 11:48 AM
    • SEQadmin2
      Advanced Sequencing Platforms Tackle Neuroscience’s Toughest Genomics Problems
      by SEQadmin2



      Genomics studies in neuroscience face a special challenge due to the brain’s complexity and scarcity of samples. Mapping changes in cell type and state using conventional next-generation sequencing methods remains challenging. Advances in technologies like single-cell sequencing, spatial transcriptomics, and long-read sequencing have opened the door to deeper studies of the brain and diseases like Alzheimer’s, amyotrophic lateral sclerosis (ALS), and schizophrenia.
      ...
      07-09-2026, 11:10 AM
    View All

    ad_right_rmr

    Collapse

    News

    Collapse
    Topics Statistics Last Post
    New Genomic Method Uncovers Ancient Hominin DNA by SEQadmin2
    Started by SEQadmin2, Yesterday, 02:55 AM
    0 responses
    10 views
    0 reactions
    		 Last Post SEQadmin2
    by SEQadmin2
    Yesterday, 02:55 AM  
    Study Captures the First Moments of DNA Replication by SEQadmin2
    Started by SEQadmin2, 07-24-2026, 12:17 PM
    0 responses
    12 views
    0 reactions
    		 Last Post SEQadmin2
    by SEQadmin2
    07-24-2026, 12:17 PM  
    Chemotherapy Leaves Detectable DNA Signatures in Childhood Tumors by SEQadmin2
    Started by SEQadmin2, 07-23-2026, 11:41 AM
    0 responses
    13 views
    0 reactions
    		 Last Post SEQadmin2
    by SEQadmin2
    07-23-2026, 11:41 AM  
    Single-Cell Atlases Skew Toward European Ancestry, Analysis Finds by SEQadmin2
    Started by SEQadmin2, 07-20-2026, 11:10 AM
    0 responses
    24 views
    0 reactions
    		 Last Post SEQadmin2
    by SEQadmin2
    07-20-2026, 11:10 AM  
    View All
    Working...