pysam

Use the AlignmentFile class to read and filter BAM files in Python, enabling mapping quality checks, region queries, and coverage calculations. It provides an ergonomic interface to htslib for scriptable genomics workflows.

The best way to query VCF variants by region in Python is using the VariantFile class with proper tabix indexing. This enables genotype querying, filtering, annotation, and sample-level analyses for reproducible genomics.

Yes, proper indexing is required before running genomic region queries. You must generate BAM/BAI, VCF/BCF tabix, and FASTA fai indexes to enable the core classes to perform region queries and variant-aware processing.

Yes, you can read, manipulate, and write CRAM alignment files. The toolkit supports reading, filtering, and writing SAM/BAM/CRAM formats to support mapping quality checks, coverage analysis, and variant-aware genomic workflows.

Access indexed FASTA sequences for NGS pipelines using the FastaFile class. It reads indexed FASTA/FASTQ data, performs region queries, and integrates with tabix-indexed data to support reproducible sequencing workflows.

BAM file region queries fail without a BAI index because the toolkit relies on proper indexing to perform region queries. Generating a BAI index enables the AlignmentFile class to execute coverage calculations and variant-aware processing.