Read depth
- Major update to calculate read depth ratios on the fly when 'normal' bam provided
- Will use the number of reads in both bams to normalise for different sequencing depths between samples
Allele frequency
- Now use the observed / expected values to adjust allele frequency for tumour purity
Get regions
- Now just take regions surrounding bps (+/- 500 currently - should adj to scale for fragment length)
- This greatly increases speed as:
- No longer need to search whole file for mates
- Now just merge reads surrounding bps (rather than all contained within bps)