Computational biology and genomics
I was updating my BAM to CRAM post spurred on by a recent comment and then I wondered whether I could store my FASTQ files as unaligned CRAM files to save space. I thought it wouldn’t be possible because the reads are unaligned and therefore we can’t make use of a reference to save space…
Last updated: 2024/12/04 TL;DR As pointed out by Colin, converting a BAM file to CRAM is simply one command: samtools view -T genome/chrX.fa -C -o eg/ERR188273_chrX.cram eg/ERR188273_chrX.bam Of note is that the reference file used to produce the BAM file is required and is used as an argument for the -T option. As for why…