pysam

This toolkit reads and writes SAM/BAM/CRAM alignments in Python by providing a Pythonic interface for genomic data I/O. It supports region queries, pileup operations, and basic quality control across these alignment formats.

Yes, you can read and write VCF/BCF variant data in Python using this toolkit. It allows you to access genotype data, INFO/FORMAT fields, and provides multi-sample support for variant analysis.

You extract specific regions from indexed FASTA sequences by performing region queries with this Python toolkit. It enables efficient sequence extraction and basic validation from indexed reference sequences.

Yes, you need to index your BAM or FASTA files for random access. This toolkit relies on index requirements to perform efficient region queries and random access for genomic data processing.

This toolkit relies on 0-based coordinate handling for genomic regions. Understanding this coordinate system is essential for accurate alignment processing, variant analysis, and sequence extraction.

Yes, you can integrate samtools and bcftools workflows into your Python scripts using this toolkit. It provides command-line tooling wrappers to interact with htslib-based tooling when needed for bioinformatics analyses.