Unconfigured Ad

Collapse
X
Collapse
 
  • Page of 1
  • Filter
  • Time
  • Show
Clear All
new posts
Previous template Next
  • Nick Bell
    Junior Member
    • Jan 2014
    • 4
    #1

    VCFtools filtering problem

    I'm having some issues filtering individuals out with a GQ below a given threshold.

    Using the command ./vcftools --vcf AST.txt --minGQ 10 --indv --recode
    I get 0 individuals kept.

    If I run it without the --indv flag it turns all my genotypes to ./.

    Any ideas?
    Tags: depth, filtering, quality filtering, vcftools
  • TiborNagy
    Senior Member
    • Mar 2010
    • 329
    #2
    Yes, because you forget to set the parameter for example: --indv NA12878

    Comment

    • Nick Bell
      Junior Member
      • Jan 2014
      • 4
      #3
      I realise now that I misinterpreted entirely what the --indv flag meant. I wanted to filter each and every individual by it's quality, not just one!

      Comment

      Previous template Next

      Latest Articles

      Collapse
      • SEQadmin2
        Advanced Sequencing Platforms Tackle Neuroscience’s Toughest Genomics Problems
        by SEQadmin2


        Genomics studies in neuroscience face a special challenge due to the brain’s complexity and scarcity of samples. Mapping changes in cell type and state using conventional next-generation sequencing methods remains challenging. Advances in technologies like single-cell sequencing, spatial transcriptomics, and long-read sequencing have opened the door to deeper studies of the brain and diseases like Alzheimer’s, amyotrophic lateral sclerosis (ALS), and schizophrenia.

        Probing...
        Today, 11:10 AM
      • SEQadmin2
        Cancer Drug Resistance: The Lingering Barrier to Rising Survival
        by SEQadmin2



        Cancer survival rates have significantly increased in the last few decades in the United States, reaching a combined 70% 5-year survival rate by 2021. Behind this number, there are years of research to find new therapies, drug targets, and early detection methods. But there is one core challenge that keeps slowing down these advances, and it’s about drug resistance.

        There is no single reason why many patients don’t respond to treatment as expected. Cancer is...
        Yesterday, 05:17 AM
      • GATTACAT
        Reply to Nine Things a Sample Prep Scientist Thinks About Before Sequencing
        by GATTACAT
        Love this - good data definitely starts from good input, and poor input can only give relatively poor data. I particularly like the mention of Nanodrop/absorbance based methods for quantification. It's such a toss up if you'll get an accurate reading or what amounts to a randomly generated number, and a lot of library/sequencing related issues can be traced back to poor quant.
        07-01-2026, 11:43 AM
      View All

      ad_right_rmr

      Collapse

      News

      Collapse
      Topics Statistics Last Post
      New Analysis Splits Leukemia Into 16 Epigenomic Subgroups by SEQadmin2
      Started by SEQadmin2, Today, 10:04 AM
      0 responses
      7 views
      0 reactions
      		 Last Post SEQadmin2
      by SEQadmin2
      Today, 10:04 AM  
      Genome-Wide CRISPR Screen Uncovers Unlikely Psoriasis Target by SEQadmin2
      Started by SEQadmin2, Yesterday, 10:08 AM
      0 responses
      6 views
      0 reactions
      		 Last Post SEQadmin2
      by SEQadmin2
      Yesterday, 10:08 AM  
      Engineered Protein Motor Takes Its First Steps Along DNA Track by SEQadmin2
      Started by SEQadmin2, 07-07-2026, 11:05 AM
      0 responses
      9 views
      0 reactions
      		 Last Post SEQadmin2
      by SEQadmin2
      07-07-2026, 11:05 AM  
      High-Resolution Sequencing Exposes Hidden Toxoplasma Diversity by SEQadmin2
      Started by SEQadmin2, 07-02-2026, 11:08 AM
      0 responses
      31 views
      0 reactions
      		 Last Post SEQadmin2
      by SEQadmin2
      07-02-2026, 11:08 AM  
      View All
      Working...