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.
Indel_only is a noddy exploration that simply removes all qualities except those within D distance of an indel.
Crumble performs a more complete trial. It uses a simple heterozygous consensus algorithm (ripped out of 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.
It also keeps all quality values for reads with mapping quality 0 (they may need to be realigned elsewhere) and within the proximity of any uncertain indel calls, where "proximity" is determined by a simply short tandem repeat search.
pipeline.sh is a noddy shell script to run samtools mpileup / bcftools call and freebayes on a sam/bam file and compares the results against a known truth set. Earlier results from some of these can be seen in BENCHMARKS_chr20, although this is now a little out of date.