Variant Calling using BCFTOOLS | BCFTOOLS Tutorial | Germline variant calling

This tutorial shows you how to call variants in sequence data using bcftools

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source of data
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6639603/
sra-database
https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=ERR3335404

Input Files
read 1
http://ftp.sra.ebi.ac.uk/vol1/run/ERR333/ERR3335404/P7741_R1.fastq.gz
read 2
http://ftp.sra.ebi.ac.uk/vol1/run/ERR333/ERR3335404/P7741_R2.fastq.gz
reference genome
https://www.ncbi.nlm.nih.gov/nuccore/CP000325.1
accession id for reference genome
CP000325.1

Documentation of the tools
samtools
http://www.htslib.org/doc/samtools-flagstat.html
bcftools
http://samtools.github.io/bcftools/bcftools.html#mpileup
https://samtools.github.io/bcftools/bcftools.html
bwa
http://bio-bwa.sourceforge.net/
sickle
https://github.com/najoshi/sickle

Setting up your PC

How to install Anaconda
Linux https://youtu.be/AshsPB3KT-E
MacOS https://youtu.be/Obl6oyh5S58 - GUI Installer
https://youtu.be/HdQoR5QqjoY - Command line installer

How to install bcftools
Compile the source code: https://youtu.be/EJGz3yryrPo
Using anaconda:https://youtu.be/BLhVqBXL_v4

Chapters
00:10 intro
01:35 install tools using conda
05:22 download sequence reads using wget
09:30 download the reference genome using your browser
11:04 download the reference genome using python
15:29 trim the raw reads using sickle
21:03 index the reference genome using bwa index command
24:11 genome mapping using bwa
26:53 convert the sam file to bam file using samtools
28:46 sort the bam file using samtools
29:42 map and sort using a one liner command
32:21 get the mapping statistics using samtools
35:33 get the converage information for bases and calculate genotype likelyhoods
39:18 call variants using bcftools
41:08 post-vcf analysis using bcftools


#bioinformatics #genome #genomics #linuxforbeginners #genomesequencing



Commands used in this tutorial
bwa index
bwa mem
samtools view
samtools sort
samtools index
samtools flagstat
bcftools mpileup
bcftools call
bcftools view