Seqanswers Leaderboard Ad

Collapse
X
 
  • Filter
  • Time
  • Show
Clear All
new posts
  • mcrusch
    Junior Member
    • Mar 2011
    • 6

    GRCh38 no alt using latest patch

    We would like to take advantage of the latest patch of GRCh38, but we also want to use the no alt analysis set. From the FTP links on the GRC site, I can only see the "analysis_set" versions for the base GRCh38, not the patched versions. Is anybody else using patched no alt (or other analysis set versions)? If so, how are you doing it?

    Sidebar: more general question: of all of the versions/flavors avaliable, what are people using?

    So far, I've thought of:
    1. Downloading the patched version and manually removing sequences I don't want and renaming to chr1, chr2, etc. The problem is that this doesn't get me the same masking as no alt, and I'm concerned of the possibility of doing something differently than the norm, which can cause problems if we're processing BAMs from somewhere else.

    2. Create an actual patch file by diffing the base and patched version, and apply that patch to the no alt.

    Both of these feel very wrong, and I'm thinking there has to be a best practice (or at least a better one).

Latest Articles

Collapse

  • seqadmin
    Pathogen Surveillance with Advanced Genomic Tools
    by seqadmin




    The COVID-19 pandemic highlighted the need for proactive pathogen surveillance systems. As ongoing threats like avian influenza and newly emerging infections continue to pose risks, researchers are working to improve how quickly and accurately pathogens can be identified and tracked. In a recent SEQanswers webinar, two experts discussed how next-generation sequencing (NGS) and machine learning are shaping efforts to monitor viral variation and trace the origins of infectious...
    03-24-2025, 11:48 AM
  • seqadmin
    New Genomics Tools and Methods Shared at AGBT 2025
    by seqadmin


    This year’s Advances in Genome Biology and Technology (AGBT) General Meeting commemorated the 25th anniversary of the event at its original venue on Marco Island, Florida. While this year’s event didn’t include high-profile musical performances, the industry announcements and cutting-edge research still drew the attention of leading scientists.

    The Headliner
    The biggest announcement was Roche stepping back into the sequencing platform market. In the years since...
    03-03-2025, 01:39 PM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, 03-20-2025, 05:03 AM
0 responses
49 views
0 reactions
Last Post seqadmin  
Started by seqadmin, 03-19-2025, 07:27 AM
0 responses
57 views
0 reactions
Last Post seqadmin  
Started by seqadmin, 03-18-2025, 12:50 PM
0 responses
50 views
0 reactions
Last Post seqadmin  
Started by seqadmin, 03-03-2025, 01:15 PM
0 responses
201 views
0 reactions
Last Post seqadmin  
Working...