What is a CRAM file?

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A CRAM file contains your DNA reads already aligned to the GRCh37 reference genome: it shows where each fragment is located in the genome, together with quality data. It represents a processing stage after FASTQ, in a compressed format that takes up much less space. 

It is used to examine specific regions of the genome, analyse coverage, identify variants or validate findings. To read it, you need bioinformatics tools such as samtools, bcftools or IGV, and the GRCh37 reference genome, the same one used for alignment and essential for decompression. Indicative requirements: Linux or macOS (on Windows, through WSL or other compatible tools), 32 GB of RAM or more, and sufficient storage space.