bcftools

bcftools is a collection of command-line utilities for processing variant call format (VCF) and its binary form (BCF). It is part of the SAMtools/HTSlib ecosystem and relies on HTSlib for reading and writing compressed VCF/BCF files, enabling efficient access to large Variant Call datasets.

The suite provides a range of functions for common variant analysis tasks. Core operations include viewing and subsetting VCF/BCF files, applying filters based on INFO and FORMAT fields, querying specific data fields, annotating records with additional information, normalizing and left-aligning indels, and merging multiple VCFs. It also offers tools to index files for fast region-based querying and to generate summary statistics from variant data. In addition, bcftools can produce a consensus sequence from a VCF and a reference when combined with appropriate workflows.

Typical workflows involve using bcftools view to extract variants from a region or sample set, bcftools filter or bcftools query to refine and summarize data, bcftools norm to standardize representation of variants, and bcftools annotate or bcftools merge to integrate information from multiple sources or files. The tools are designed to handle large-scale sequencing data and support multi-threaded operation, with many commands accepting a multi-thread flag to speed processing on big datasets.

bcftools works with VCF and BCF formats, supports indexed and compressed files, and is widely used in genomics pipelines for variant data processing, quality control, and preparation for downstream analysis.