Unconfigured Ad

Collapse
X
 
  • Time
  • Show
Clear All
new posts
  • XeroxHero69
    Member
    • Apr 2019
    • 12

    #1

    How to regenerate an index file for a gzipped vcf file?

    I have a large vcf file with genomic data (330 GB) and an index file that accompanies it. I ran the command:

    bcftools view -f PASS --threads 8 -r chr9:55252802-55252810 -o output.vcf.gz -O z 722g.990.SNP.INDEL.chrAll.vcf.gz

    I get:

    [W::hts_idx_load2] The index file is older than the data file: 722g.990.SNP.INDEL.chrAll.vcf.gz.tbi
    [W::hts_idx_load2] The index file is older than the data file: 722g.990.SNP.INDEL.chrAll.vcf.gz.tbi


    I was told that I need to regenerate my index file using Tabix. I have tried the following command that seemed to work for someone else having a similar problem:

    tabix -p vcf 722g.990.SNP.INDEL.chrAll.vcf.gz

    but it returned:

    tbx_index_build failed: 722g.990.SNP.INDEL.chrAll.vcf.gz

    I am not quite sure what command I should be using to regenerate my index file. Any help is greatly appreciated!

Latest Articles

Collapse

  • 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, detection...
    Today, 06:46 AM
  • 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

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by SEQadmin2, 10-28-2026, 09:57 AM
0 responses
23 views
0 reactions
Last Post SEQadmin2  
Started by SEQadmin2, 10-28-2026, 09:51 AM
0 responses
15 views
0 reactions
Last Post SEQadmin2  
Started by SEQadmin2, 10-22-2026, 11:13 AM
0 responses
68 views
0 reactions
Last Post SEQadmin2  
Started by SEQadmin2, 10-22-2026, 10:48 AM
0 responses
48 views
0 reactions
Last Post SEQadmin2  
Working...