Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • Filtering out individual genotype calls with too HIGH read depth from VCF

    I have VCF files generated from GATK's HaplotypeCaller. One file per each of 20 individuals. These VCF files will be combined into a multi-sample gVCF for joint genotyping using GenotypeGVCFs (GATK), producing a vcf.gz file including all variable positions across the individuals.

    I would like to set a filter to remove certain variants. The tricky part is that this filter is not a global filter, meaning, the filtering threshold should be set differently for each individual. Specifically, I'm looking to exclude any genotype (variant) call *within an individual* that has more than 4-times the average read depth of *that individual*.

    How do I achieve such filtering? Can this be done on the combined vcf-file (or even the variants vcf file), or do I have to do such filtering before combining individual VCF files into one?
    And, how do I implement this filter? I cannot think of any tool that allows me to filter out positions with a too high read depth, and particularly not if the respective threshold depends on the genome-wide average.

    Thank you for your help!

  • #2
    That would require some scripting, I think. vcftools can filter for sites within a range of read depth, so you could:
    extract one individual with vcftools --indv
    find the mean depth with vcftools --depth
    filter that individual with --max-meanDP

    but at that point I would just parse the vcf with a scripting language.
    Providing nextRAD genotyping and PacBio sequencing services. http://snpsaurus.com

    Comment

    Latest Articles

    Collapse

    • seqadmin
      Genetic Variation in Immunogenetics and Antibody Diversity
      by seqadmin



      The field of immunogenetics explores how genetic variations influence immune responses and susceptibility to disease. In a recent SEQanswers webinar, Oscar Rodriguez, Ph.D., Postdoctoral Researcher at the University of Louisville, and Ruben Martínez Barricarte, Ph.D., Assistant Professor of Medicine at Vanderbilt University, shared recent advancements in immunogenetics. This article discusses their research on genetic variation in antibody loci, antibody production processes,...
      11-06-2024, 07:24 PM
    • seqadmin
      Choosing Between NGS and qPCR
      by seqadmin



      Next-generation sequencing (NGS) and quantitative polymerase chain reaction (qPCR) are essential techniques for investigating the genome, transcriptome, and epigenome. In many cases, choosing the appropriate technique is straightforward, but in others, it can be more challenging to determine the most effective option. A simple distinction is that smaller, more focused projects are typically better suited for qPCR, while larger, more complex datasets benefit from NGS. However,...
      10-18-2024, 07:11 AM

    ad_right_rmr

    Collapse

    News

    Collapse

    Topics Statistics Last Post
    Started by seqadmin, 11-08-2024, 11:09 AM
    0 responses
    221 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 11-08-2024, 06:13 AM
    0 responses
    163 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 11-01-2024, 06:09 AM
    0 responses
    80 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 10-30-2024, 05:31 AM
    0 responses
    27 views
    0 likes
    Last Post seqadmin  
    Working...
    X