pysam

To fetch alignments from a BAM file, use Python bindings to htslib for region-based queries. This approach supports reading SAM/BAM/CRAM formats, allowing you to open an alignment file, specify genomic coordinates, and programmatically extract matching sequence reads.

Yes, you can read and write variant files in VCF/BCF formats to perform filtering or annotation. This provides programmatic access to variant records, enabling customized query logic and modification for downstream bioinformatics validation workflows.

Extracting reference sequences from FASTA files requires accessing the sequences programmatically and querying by region. This allows you to retrieve exact nucleotide strings for specified coordinates, integrating reference data with alignment or variant analysis.

Yes, the toolkit supports CRAM files alongside SAM, BAM, VCF, BCF, FASTA, and FASTQ. This enables cross-format data integration for end-to-end bioinformatics pipelines, including quality control, coverage analysis, and variant validation.

Pileup analysis is performed by reading alignment files and generating per-base stackups at specified genomic coordinates. This allows you to inspect coverage depth, base calls, and alignment mismatches across sequencing reads for quality control.