Unconfigured Ad

Collapse
X
Collapse
 
  • Page of 1
  • Time
  • Show
Clear All
new posts
Previous template Next
  • XeroxHero69
    Member
    • Apr 2019
    • 12
    #1

    bcftools output type not recognized

    I am trying to find a single SNP on a bunch of dog genomes in a compressed vcf file (vcf.gz) and I have been using bcftools to do so. I posted before on what command I should use and got some help:

    bcftools view -f PASS --threads 8 -T canine.bed -o 722g.990.SNP.INDEL.chrAll.vcf.gz -O 722g.990.SNP.INDEL.chrAll.vcf.bgz

    I created an empty file for the output file but I get the error:

    The output type "722g.990.SNP.INDEL.chrAll.vcf.bgz" not recognised

    If anyone knows what's going on here and what I'm doing wrong, I would greatly appreciate it! Thank you
    Last edited by XeroxHero69; 05-07-2019, 10:41 AM. Reason: added link
    Tags: bcftools, helpmeplz, linux, vcf
    • finswimmer
      Member
      • Oct 2016
      • 60
      #2
      Changing the file extenstion .bgz to .gz should solve the problem.

        Comment

        Previous template Next

        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
        View All

        ad_right_rmr

        Collapse

        News

        Collapse
        Topics Statistics Last Post
        Exeter-Led Study Maps What an Average Human Genome Looks Like by SEQadmin2
        Started by SEQadmin2, 10-22-2026, 11:13 AM
        0 responses
        27 views
        0 reactions
        		 Last Post SEQadmin2
        by SEQadmin2
        10-22-2026, 11:13 AM  
        Long-Read Sequencing Uncovers Cancer Mutations Conventional Testing Missed by SEQadmin2
        Started by SEQadmin2, 10-22-2026, 10:48 AM
        0 responses
        20 views
        0 reactions
        		 Last Post SEQadmin2
        by SEQadmin2
        10-22-2026, 10:48 AM  
        Mayo Clinic-Led Study Detects DNA Mutations Across Noncancerous Tissues by SEQadmin2
        Started by SEQadmin2, 10-15-2026, 10:52 AM
        0 responses
        36 views
        0 reactions
        		 Last Post SEQadmin2
        by SEQadmin2
        10-15-2026, 10:52 AM  
        Study Finds Chromatin Motion Holds Steady Until Cells Face Stress by SEQadmin2
        Started by SEQadmin2, 10-14-2026, 05:39 AM
        0 responses
        43 views
        0 reactions
        		 Last Post SEQadmin2
        by SEQadmin2
        10-14-2026, 05:39 AM  
        View All
        Working...