BCFTools Tutorial for Splitting VCFs based on Sample IDs | BCFTools view Example
Download the bash script with codes: / 85644874
BCFTools Tutorial for Splitting or Subsetting VCFs based on sample IDS
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How to Install BCFTOOLS
How to install bcfools
conda: • Install BCFTOOLS in Linux using anaconda |...
build from source: • How to install BCFTOOLS in any Linux Machi...
How to install conda: • How I install and configure Anaconda in a...
• Install , Configure and Run Anaconda in a...
How to install mamba: • Install , Configure and Run Mamba & Conda...
Download the example data
https://github.com/vappiah/bioinfodat...
https://github.com/vappiah/bioinfodat...
BCFTOOLS documentation : https://samtools.github.io/bcftools/b...
BCFTOOLS Plugins: https://samtools.github.io/bcftools/h...
GATK SelectVariants : https://gatk.broadinstitute.org/hc/en...
Chapters
00:00 Intro
00:09 Where to get the bash script with codes for this tutorial
00:23 PC Requirement
01:02 Create a working directory cd into it
01:15 Download the example data
02:48 Splitting begins
03:05 Get the sample ids with bcftools
07:11 Index the vcf file
07:44 Split the vcf file using bcftools +split
09:50 Count the number of variants per sample using bcftools
12:39 Get the True Variants
16:21 Get the variant for multiple samples
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