Unconfigured Ad

Collapse
X
Collapse
 
  • Page of 1
  • Time
  • Show
Clear All
new posts
Previous template Next
  • jwhite
    Member
    • Jun 2012
    • 33
    #1

    extract FASTA from BAM

    Hi Folks,

    Does anyone know the samtools command to extract a consensus sequence in FASTA format from a BAM file? Not the reference sequence (with faidx) but the consensus of the reads in a region.

    Thanks for any help you can supply.

    Cheers,
    Joe White
    Tags: None
    • GenoMax
      Senior Member
      • Feb 2008
      • 7142
      #2
      Consensus FASTA from BAM files - SEQanswers
      http://seqanswers.com/forums/showthread.php?t=11536
      Discussion of next-gen sequencing related bioinformatics: resources, algorithms, open source efforts, etc


      You will need to combine suggestions from posts in the thread above.

        Comment

        Previous template Next

        Latest Articles

        Collapse
        • kinpict.com
          Reply to 16S/ITS Profiling vs. Shotgun Metagenomics: What Changes in Your Workflow?
          by kinpict.com
          The part about this topic feels surprisingly grounded, and the details on the page is the bit that made me slow down. I’d keep <a href="https://kinpict.com/">ai family photo generator</a> bookmarked for later.
          Today, 06:37 PM
        • SEQadmin2
          16S/ITS Profiling vs. Shotgun Metagenomics: What Changes in Your Workflow?
          by SEQadmin2





          NGS has revolutionized clinical microbiology by offering new ways to identify and surveil pathogens without prior knowledge of the target. One popular approach is 16S rRNA and ITS amplicon sequencing, which targets specific microbial markers. But studies are increasingly incorporating shotgun metagenomics, a technique that sequences all DNA from a sample without targeting specific microbial markers. This approach allows more detailed taxonomic classification,...
          10-30-2026, 06:46 AM
        View All

        ad_right_rmr

        Collapse

        News

        Collapse
        Topics Statistics Last Post
        Gene Copies Once Dismissed as Junk DNA Shape Animal Adaptation and Human Disease by SEQadmin2
        Started by SEQadmin2, 11-12-2026, 07:59 AM
        0 responses
        26 views
        0 reactions
        		 Last Post SEQadmin2
        by SEQadmin2
        11-12-2026, 07:59 AM  
        WashU Medicine Study Verifies Methods for Tracking Genetic Mosaicism by SEQadmin2
        Started by SEQadmin2, 11-05-2026, 09:25 AM
        0 responses
        35 views
        0 reactions
        		 Last Post SEQadmin2
        by SEQadmin2
        11-05-2026, 09:25 AM  
        HuBMAP Portal Offers Free Access to Single-Cell Data from Healthy Human Tissues by SEQadmin2
        Started by SEQadmin2, 11-03-2026, 11:54 AM
        2 responses
        55 views
        0 reactions
        		 Last Post kinpict.com
        by kinpict.com
        Today, 06:49 PM  
        Genome Sequencing Reveals Large, Repeat-Rich DNA in Trapdoor Spider Named for Stephen Colbert by SEQadmin2
        Started by SEQadmin2, 10-28-2026, 09:57 AM
        0 responses
        175 views
        0 reactions
        		 Last Post SEQadmin2
        by SEQadmin2
        10-28-2026, 09:57 AM  
        View All
        Working...