WGS Variant Calling: Variant Filtering and Annotation - Part 2 | Detailed NGS Analysis Workflow скачать в хорошем качестве

WGS Variant Calling: Variant Filtering and Annotation - Part 2 | Detailed NGS Analysis Workflow

This is the detailed workflow tutorial on how to filter variants and annotate them using GATK's Funcotator tool. In this video I discuss the need of filtering and annotating variants, the questions we may ask once we call variants, two approaches to filter variants i.e. Variant Quality Score Recalibration (VQSR) & hard filtering, the data sources available, genotype refinement and finally talking about Funcotator. Further, I demonstrate how to filter variants at the site level as well apply genotype filters and annotating variants using Funcotator. Lastly, I demonstrate how to wrangle the output from Funcotator and get the annotations in a tabular format which is helpful for further processing and visualization. I hope you find this video helpful! Leave your thoughts in the comment section below! ▸ Code: https://github.com/kpatel427/YouTubeT... ▸ Part 1 of this video:    • WGS Variant Calling: Variant calling with ...   ▸ VCF file format video:    • Understanding File Formats in Bioinformati...   ▸ GATK hard-filters recommendations for germline variants: https://gatk.broadinstitute.org/hc/en... Chapters: 0:00 Intro 0:43 Overview of variant calling steps 1:34 Questions we may want to ask after calling variants 3:00 Variant data sources 5:16 Two approaches to filter variants 8:38 Hard filtering: Site-level filtering 9:14 Hard filtering: Sample-level filtering 10:15 Genotype Refinement 10:54 Data used for today’s demo 11:22 Pre-requisites 12:22 Filtering SNPs 16:54 Filtering INDELS 17:35 Understanding output after filtering (FILTER column) 19:19 Select variants that passed filters 20:39 Exclude variants that failed genotype filters 25:49 GATK Funcotator tool 28:10 Funcotator data sources 29:59 Annotate variants using Functotator 32:07 Understanding output after annotation (Funcotator output) 33:45 Getting annotations into a tabular format You can show your support and encouragement by buying me a coffee: https://www.buymeacoffee.com/bioinfor... To get in touch: Website: https://bioinformagician.org/ Github: https://github.com/kpatel427 Email: khushbu_p@hotmail.com #bioinformagician #bioinformatics #funcotator #variantcalling #variants #gatk #vcf #gvcf #haplotype #alleles #geneticvariants #mutations #gff3 #gff #gtf #sam #bam #phred #fasta #fastq #singlecell #10X #ensembl #biomart #annotationdbi #annotables #affymetrix #microarray #affy #ncbi #genomics #beginners #tutorial #howto #omics #research #biology #GEO #rnaseq #ngs