Somatic Variant Calling with Mutect2 | GATK Best Practices Tutorial

In this tutorial, we'll take an in-depth look at the workflow for calling somatic variants using Mutect2, based on GATK's best practices. I'll guide you through the entire process of identifying somatic mutations, covering key concepts, the challenges involved, and how somatic variant calling differs from germline variant calling. Furthermore, I'll also discuss the insights that somatic variants can provide, followed by a hands-on demonstration of variant calling, filtering, and annotation.
Don't forget to like, share, and subscribe for more insightful tutorials! I look forward to your comments under the comments section!

▸ Code:
1. https://github.com/kpatel427/YouTubeTutorials/blob/main/somatic_variant_calling_get_reads_1.sh
2. https://github.com/kpatel427/YouTubeTutorials/blob/main/somatic_variant_calling_preprocessing_2.sh
3. https://github.com/kpatel427/YouTubeTutorials/blob/main/somatic_variant_calling_filtering_annotation_3.sh

▸ Germline Variant Calling using GATK’s best practice workflow PART 1: https://youtu.be/iHkiQvxyr5c?si=7uGnflCk07u-OE9p

▸ Germline Variant Calling using GATK’s best practice workflow PART 2: https://youtu.be/XZ8scaScfjw?si=aIPoPqJ4AQmMgYR9

▸ What is a VCF file?
https://youtu.be/cBDZSGf9HRE?si=LTZEniIKffnaSw9f

▸ How to get data from the GDC (TCGA) portal?
https://youtu.be/UWXv9dUpxNE?si=m4S1ANHJAiHP9vx0
Chapters:
0:00 Intro
1:15 Germline vs Somatic variants
3:08 Germline variant calling vs Somatic variant calling
4:42 Challenges in calling somatic variants
5:36 Overview of somatic variant calling workflow
6:42 Rationale behind Germline Filtering
8:01 Rationale behind Panel of Normals (PoN)
9:48 Rationale behind Contamination Estimation and Filtering
10:35 Rationale behind Read Orientation Bias
11:54 What questions do somatic variants help to answer?
12:56 Somatic variant databases
14:19 Data used for this demonstration
14:40 Things that will not be covered in this demonstration
14:56 Requirements
15:43 Data download, directory set-up and going over scripts
19:41 Calling variants using Mutect2
23:26 GetPileupSummaries to estimate cross-sample contamination
26:30 Calculate contamination
28:23 Estimate read orientation artifacts
30:08 Filter variants
31:57 Going over filtered variants
35:10 Annotating variants using Funcotator

You can show your support and encouragement by buying me a coffee:
https://www.buymeacoffee.com/bioinformagic

To get in touch:
Website: https://bioinformagician.org/
Github: https://github.com/kpatel427
Email: khushbu_p@hotmail.com
#bioinformagician #bioinformatics #liftover #ucscgenomebrowser #crossmap #rtracklayer #signac #atacseq #atac #seurat #singlecell #singler #illumina #bridgeamplification #sequencingbysynthesis #multiplex #alleles #10x #oxfordnanopore #pacbio #affymetrix #barcode #setseed #reproducibility #pseudorandom #singleR #singlecell #annotationdbi #reversestranded #directstranded #strandedness #survival #survminer #survivalanalysis #kaplanmeier #tcga #gdcportal #tcgaportal #nci #cran #bioconductor #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

Видео Somatic Variant Calling with Mutect2 | GATK Best Practices Tutorial канала Bioinformagician