bcftools: A Short Introduction

• ⚠️ This is a short blog post, more like an overview of the bcftools in general. For those unfamiliar with the tool, bcftools is a suite of tools used to work with variant call format (VCF) and the binary variant call format (BCF), which is the binary version of VCF files.

• ℹ️ VCF and BCF files are used to store genetic variation data. As one might expect, bcftools is widely used in genomics and bioinformatics for different purposes.

• ℹ️ Bcftools is a command-line tool and can run on various operating systems (Linux, macOS, and Windows).

👨🏼‍🏫 My BCFTOOLS Tutorials

Here is the list of bcftools tutorials that I have created so far:

1. bcftools sort: How do you sort VCF/BCF files?

2. bcftools index: How to create index for VCF files?

3. bcftools query: How do you extract specific fields from a VCF file into a text file?

4. How to Add/Remove/Annotate VCF Columns and Corresponding Field bcftools annotate: Concrete Examples

5. How To Combine Multiple VCF/BCF Files Into a Single VCF File Using the Bcftools Concat Command?

6. 🧬👩🏽‍💻 A Guide to Merging VCF and BCF Files: Your bcftools merge Tutorial

7. What’s the Difference Between Bcftools Concat and Bcftools Merge?
   

🤖 What Does bcftools Do?

bcftools provides a range of capabilities for manipulating and analyzing VCF and BCF files, including, among other things:

• 1️⃣ Converting between VCF and BCF formats

• 2️⃣ Viewing and filtering variant data stored in VCF and BCF tools

• 3️⃣ Performing data manipulation operations like merging and intersecting variant sets

• 4️⃣ Annotating variant data with additional information, such as gene and functional impact

• 5️⃣ Performing population-level analyses, such as calculating allele frequencies and Hardy-Weinberg equilibrium

🖥️ BCFTOOLS Commands

As I mentioned above, bcftools is a suite of tools or utilities (as those are described in bcftools documentation). Currently, there are 22 bcftools commands/utilities, and those are grouped into three main groups:

• 1️⃣ indexing command

• 2️⃣ VCF/BCF manipulation commands, and

• 3️⃣ VCF/BCF analysis commands.

• Indexing tools contain only one command, which is bcftools index. To learn more about this command, check out my tutorial about the bcftools index here.

• The group of VCF/BCF manipulation commands within which there are 11 commands, all listed below:

  • bcftools annotate: annotate and edit VCF/BCF files

  • bcftools concat: concatenate VCF/BCF files from the same set of samples

  • bcftools convert: convert VCF/BCF files to different formats and back

  • bcftools isec: intersections of VCF/BCF files

  • bcftools merge: merge VCF/BCF files files from non-overlapping sample sets

  • bcftools norm: left-align and normalize indels

  • bcftools plugin: user-defined plugins

  • bcftools query: transform VCF/BCF into user-defined formats

  • bcftools reheader: modify VCF/BCF header, change sample names

  • bcftools sort: sort VCF/BCF file.

  • bcftools view: VCF/BCF conversion, view, subset, and filter VCF/BCF files
    

• The group of VCF/BCF analysis commands within which there are 10 commands, all listed below:

  • bcftools call: SNP/indel calling

  • bcftools consensus: create a consensus sequence by applying VCF variants

  • bcftools cnv: HMM CNV calling

  • bcftools csq: call variation consequences

  • bcftools filter: filter VCF/BCF files using fixed thresholds

  • bcftools gtcheck: check sample concordance, detect sample swaps and contamination

  • bcftools mpileup: multi-way pileup producing genotype likelihoods

  • bcftools polysomy: detect number of chromosomal copies

  • bcftools roh: identify runs of autozygosity (HMM)

  • bcftools stats: produce VCF/BCF stats

This was the first blog post where I wanted to give you a short introduction. In every next blog post, I will present one of the above commands with practical examples. Also, as we go, I will probably expand this article with additional information and explanations.