Oxford University Press, Bioinformatics, 2(35), p. 337-339, 2018
DOI: 10.1093/bioinformatics/bty608
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Abstract Motivation The bulk of space taken up by NGS sequencing CRAM files consists of per-base quality values. Most of these are unnecessary for variant calling, offering an opportunity for space saving. Results On the Syndip test set, a 17 fold reduction in the quality storage portion of a CRAM file can be achieved while maintaining variant calling accuracy. The size reduction of an entire CRAM file varied from 2.2 to 7.4 fold, depending on the non-quality content of the original file (see Supplementary Material S6 for details). Availability and implementation Crumble is OpenSource and can be obtained from https://github.com/jkbonfield/crumble. Supplementary information Supplementary data are available at Bioinformatics online.