BAM File

A BAM (Binary Alignment/Map) file is a binary format for storing DNA sequence data that has been aligned to a reference genome. It is a compressed, binary version of the SAM (Sequence Alignment/Map) file, which is a text-based format. BAM files are widely used in bioinformatics for handling large-scale sequencing data generated from Next-Generation Sequencing (NGS) technologies. BAM files are an essential component of bioinformatics workflows for processing and analyzing high-throughput sequencing data.

Key Characteristics:

Binary Format: BAM files are more efficient in terms of storage and access speed compared to SAM files because they are compressed.
Aligned Data: They contain read sequences that have been aligned to a reference genome, along with information about the alignment (e.g., position, mapping quality, and flags indicating different attributes of the reads).
Indexable: BAM files can be indexed (.bai files), allowing rapid access to specific genomic regions without loading the entire file into memory.

Typical Uses:

Storing aligned sequencing reads
Variant calling and genome assembly
Visualizing read alignments using genome browsers like IGV (Integrative Genomics Viewer).

BAM and BAI files for your cases launched using Nostos secondary analysis can be downloaded from the case overview page for secondary analysis under "Download data" drop down menu:

In order to see the read alignment you can upload the BAM amb BAI files into your IGV desktop app and visualize the variant when clicking on the IGV logo in the AION UI:

For more information on variant visualization using IGV please visit the AION results and Manual filtering - CNVs pages.

Additional Resources:

Li, H., Handsaker, B., Wysoker, A., et al. (2009). "The Sequence Alignment/Map format and SAMtools." Bioinformatics, 25(16), 2078-2079. DOI:10.1093/bioinformatics/btp352