Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Calculating Genotype Likelihood from NGS

    Hi,
    I have human whole genome sequencing data (at 30x depth) which is already called using CASAVA. I plan to use these genotype data (>3million SNPs per individual) for quantitative trait association study. regarding the fraction of the polymorphisms which have a low coverage (e.g. < 4) should I filter these out, or it would be better to feed these low coverage data to an imputation pipeline?

  • #2
    Check the mapping quality of the reads. If the mapping quality too low, you can filter out.

    Comment


    • #3
      Originally posted by TiborNagy View Post
      Check the mapping quality of the reads. If the mapping quality too low, you can filter out.
      Is that the QUAL field in VCF? so you recommend filtering only based on QUAL and not considering GQ/read depth? i.e. what should be done if quality is good, but depth is moderate/low?

      Comment


      • #4
        Useful thread about filtering VCF files over in GATK forum: http://gatkforums.broadinstitute.org...ring-vcf-files

        Comment


        • #5
          Originally posted by GenoMax View Post
          Useful thread about filtering VCF files over in GATK forum: http://gatkforums.broadinstitute.org...ring-vcf-files
          Thanks for your response. I have gone through the suggestions provided on this link. My specific problem is with variants with good QUAL (hard filter >20~30) but low sequencing depth, which translates to lower certainty about the exact genotype. i.e. there is already some evidence to rule-out REF/REF genotype, but not enough reads to specify REF/ALT vs ALT/ALT.

          Is there any recommendation/paper regarding NGS genotyping and association studies? Overall, Does it make sense to filter based on both QUAL and Depth/GQ parameters?

          Comment

          Latest Articles

          Collapse

          • seqadmin
            Quality Control Essentials for Next-Generation Sequencing Workflows
            by seqadmin




            Like all molecular biology applications, next-generation sequencing (NGS) workflows require diligent quality control (QC) measures to ensure accurate and reproducible results. Proper QC begins at nucleic acid extraction and continues all the way through to data analysis. This article outlines the key QC steps in an NGS workflow, along with the commonly used tools and techniques.

            Nucleic Acid Quality Control
            Preparing for NGS starts with isolating the...
            02-10-2025, 01:58 PM
          • seqadmin
            An Introduction to the Technologies Transforming Precision Medicine
            by seqadmin


            In recent years, precision medicine has become a major focus for researchers and healthcare professionals. This approach offers personalized treatment and wellness plans by utilizing insights from each person's unique biology and lifestyle to deliver more effective care. Its advancement relies on innovative technologies that enable a deeper understanding of individual variability. In a joint documentary with our colleagues at Biocompare, we examined the foundational principles of precision...
            01-27-2025, 07:46 AM

          ad_right_rmr

          Collapse

          News

          Collapse

          Topics Statistics Last Post
          Started by seqadmin, 02-07-2025, 09:30 AM
          0 responses
          54 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 02-05-2025, 10:34 AM
          0 responses
          88 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 02-03-2025, 09:07 AM
          0 responses
          68 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 01-31-2025, 08:31 AM
          0 responses
          44 views
          0 likes
          Last Post seqadmin  
          Working...
          X