Unconfigured Ad

Collapse
X
Collapse
 
  • Page of 1
  • Time
  • Show
Clear All
new posts
Previous template Next
  • nikkiat
    Junior Member
    • Apr 2012
    • 1
    #1

    merge-vcf yielding '.' for ALT

    I converted some files to vcf with my own script and am trying to merge them using vcf-merge. Each file is its own sample. They appear to merge fine, but I am given '.' as the ALT instead of 'C,T' or whatever it should be.

    Lines from one of the input files:
    #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 27MS2
    chr1 67403777 rs6682922 C T . RD DB GT:VF:GN:FX .|.:H:IL23R:Promoter
    chr1 67403999 . T C . RD . GT:VF:GN:FX .|.:B:IL23R:Promoter

    Lines from the output file:
    #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 27MS2 27MS3 27MS4
    chr1 67403777 rs6682922 C . . RD AC=0;AN=0;DB;SF=0f,1f,2f GT:FX:VF:GN .|.:Promoter:47.0707:IL23R .|.:Promoter:60.2070:IL23R .|.:Promoter:38.0866:IL23R
    chr1 67403999 . T . . RD AC=0;AN=0;SF=0f GT:FX:VF:GN .|.:Promoter:8.2149:IL23R . .

    Why is it displaying '.' instead of the ALTs?
    Last edited by nikkiat; 04-20-2012, 09:03 AM.
    Tags: '.', vcf-merge, vcf-tools
    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
    38 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
    44 views
    0 reactions
    		 Last Post SEQadmin2
    by SEQadmin2
    10-14-2026, 05:39 AM  
    View All
    Working...