Crumble

Exploration of controlled loss of quality values for compressing CRAM files

This directory contains some experimental tools that read a SAM/BAM/CRAM file, compute which confidence values to keep and which to omit, and emit a new file with most qualities removed.

See INSTALL for compilation and installation instructions.

Crumble uses a simple heterozygous consensus algorithm (taken from gap5) in a couple of modes to produce a consensus call with a confidence. If the calls are highly confident then it throws away the quality values (setting them to fixed high or low depending on whether they agree with the call), otherwise it keeps them.

To control the output format use -O FMT. This may also be used to add additional parameters. Eg "-O bam,nthreads=8" may be used to enable multi-threaded BGZF compression when writing the BAM file.

A paper is available with comprehensive benchmarks:

http://dx.doi.org/10.1093/bioinformatics/bty608

Independent benchmarks are also available in a DNAnexus blog post:

https://blog.dnanexus.com/2018-07-23-breaking-down-crumble/