Small-Variant Calling and Annotation
Channel: Bioinformatics DotCa
Date: 28/05/2018

This is the fourth module of the Informatics on High-Throughput Sequencing Data 2018 workshop hosted by the Canadian Bioinformatics Workshops at the Ontario Institute for Cancer Research. This session is by Mathieu Bourgey from the Canadian Centre for Computational Genomics at McGill University. 

Table of Contents:

00:36 - Learning Objectives of Module
01:55 - {
02:06 - Compute Canada
03:04 - Tools, pipelines and data on Compute Canada
03:54 - GenAP
04:27 - }
04:28 - Genome re-sequencing
05:53 - Simplified variant analysis workflow
06:26 - Main analysis steps
06:48 - Importance of quality control
08:06 - Main analysis steps
08:15 - SNV calling
08:20 - SNPs
08:45 - SNP Discovery: Goal
10:26 - Base quality
10:33 - SNP Discovery: Base Qualities
11:18 - SNP and genotype calling workflow
13:51 - 
14:01 - SNP and genotype calling workflow
14:39 - 
15:26 - 
15:47 - Strategies that improve variant calling
16:24 - Strategies that improve variant calling
16:28 - Local realignement
18:14 - Strategies that improve variant calling
18:23 - Duplicate marking
19:15 - Strategies that improve variant calling
19:16 - Base quality recalibration
19:40 - Strategies that improve variant calling
19:54 - Using haplotypes for base calling
21:10 - Impact of using multi-samples and haplotype information
21:43 - Handling Trios
23:01 - 
24:17 - The variant format : vcf
28:59 - Variant filtering and annotation
29:00 - The variant format : vcf
29:24 - Variant filtering and annotation
29:26 - Variant filtering
29:28 - Variant filtering and annotation
29:29 - The variant format : vcf
30:49 - Variant filtering and annotation
30:53 - The variant format : vcf
32:08 - Variant filtering and annotation
32:10 - The variant format : vcf
35:57 - Variant filtering and annotation
36:08 - Variant filtering
38:42 - Variant Quality Recalibration
40:16 - QC: HapMap &amp; dbSNP
40:18 - Variant Quality Recalibration
41:28 - QC: HapMap &amp; dbSNP
42:19 - Variant annotation 
44:04 - Annotating variants with SnpEff
44:31 - Variant annotation 
46:07 - Annotating variants with SnpEff
46:07 - 
46:11 - Annotating variants with SnpEff
46:12 - Variant annotation 
47:10 - Annotating variants with SnpEff
47:14 - 
47:14 - Annotating variants with SnpEff
47:43 - 
48:40 - Add-on
48:44 - VCF visualization in IGV
49:13 - General metrics
49:29 - SNV statistics
49:40 - Lab time!
53:15 - SNV statistics
53:26 - General metrics
53:27 - VCF visualization in IGV
53:27 - Add-on
53:27 - 
53:28 - Annotating variants with SnpEff
53:28 - Variant annotation 
53:28 - QC: HapMap &amp; dbSNP
53:29 - Variant filtering
53:29 - Variant filtering and annotation
53:29 - The variant format : vcf
53:30 - 
53:30 - Handling Trios
53:31 - Impact of using multi-samples and haplotype information
53:31 - Using haplotypes for base calling
53:31 - Strategies that improve variant calling
53:31 - Base quality recalibration
53:32 - Strategies that improve variant calling
53:32 - Duplicate marking
53:33 - Strategies that improve variant calling
53:33 - Local realignement
55:30 - Strategies that improve variant calling
55:30 - Local realignement
55:31 - Strategies that improve variant calling
55:31 - Duplicate marking
55:32 - Strategies that improve variant calling
55:32 - Base quality recalibration
55:33 - Strategies that improve variant calling
55:33 - Using haplotypes for base calling
55:33 - Impact of using multi-samples and haplotype information
55:34 - Handling Trios
55:35 - 
55:36 - The variant format : vcf
57:21 - Variant filtering and annotation
57:29 - The variant format : vcf