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