Header Leaderboard Ad


Filtering methods for samtools or GATK



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

  • Filtering methods for samtools or GATK

    Hello everyone!

    I just started my PhD and my level of expertise is fairly low about bioinformatics! Is there any advice regarding different coverage levels? ( 10x vs 50x or more ).
    I would need simple instructions for filtering using either samtools or GATK. We are looking for ROH (runs of homozygosity) so we need to avoid variants being called where they are not genuine. I tried to use MQ < 40 and DP>200 but not sure if they are right or fixed.

    Thanks for your answer!


Latest Articles


  • seqadmin
    A Brief Overview and Common Challenges in Single-cell Sequencing Analysis
    by seqadmin

    ​​​​​​The introduction of single-cell sequencing has advanced the ability to study cell-to-cell heterogeneity. Its use has improved our understanding of somatic mutations1, cell lineages2, cellular diversity and regulation3, and development in multicellular organisms4. Single-cell sequencing encompasses hundreds of techniques with different approaches to studying the genomes, transcriptomes, epigenomes, and other omics of individual cells. The analysis of single-cell sequencing data i...

    01-24-2023, 01:19 PM
  • seqadmin
    Introduction to Single-Cell Sequencing
    by seqadmin
    Single-cell sequencing is a technique used to investigate the genome, transcriptome, epigenome, and other omics of individual cells using high-throughput sequencing. This technology has provided many scientific breakthroughs and continues to be applied across many fields, including microbiology, oncology, immunology, neurobiology, precision medicine, and stem cell research.

    The advancement of single-cell sequencing began in 2009 when Tang et al. investigated the single-cell transcriptomes
    01-09-2023, 03:10 PM