V00397 - SOP for germline variant calling and VCF generation скачать в хорошем качестве

V00397 - SOP for germline variant calling and VCF generation

Identify germline genetic variants with professional accuracy using this standardized bioinformatics workflow for NGS data. This video tutorial details the essential steps required to process raw paired-end FASTQ files into high-quality filtered VCF files. We begin by outlining the responsibilities of the bioinformatics team and the necessary software suite, including tools like BWA-MEM for alignment and GATK for variant calling. The procedure starts with raw read quality assessment via FastQC and continues through adapter trimming with fastp to ensure only high-quality data enters the pipeline. You will learn how to map reads to the hg38 reference genome and perform critical post-alignment processing such as duplicate marking with Picard and optional base quality score recalibration. The heart of the tutorial focuses on the GATK HaplotypeCaller for single-sample variant identification, followed by rigorous hard filtering of SNPs and Indels to minimize false positives. We also highlight the importance of quality control metrics, including a mapping rate greater than 95% and mean coverage thresholds to ensure the reliability of your findings. Finally, the video covers best practices for data storage, ensuring that raw FASTQ, processed BAM, and final VCF files are archived alongside their respective pipeline logs. Whether you are working on Whole Genome or Whole Exome Sequencing, this SOP provides the technical depth and clear instructions needed to generate publication-ready genomic data for any genetic project . #Bioinformatics #NGS #Genomics #VCF #GATK #DataScience #Genetics #WGS #SOP #DNAAnalysis