From Twist:
Using our default filters it looks like we would be able to cover 80.39% of your targets, with the following regions filtered out: bed file
We can recover a few more targets if we allow shifting of probes but the following would still remain uncovered: bed file
We assessed the sites the could not be reliably targeted (without 'shifting'). Below we refer to these as 'uncovered'.
Rscript src/clarify.r \
../panel.csv \
../ancestry/output/sites.csv \
../episcores/episcore-sites.csv \
all_target_segments_not_covered_by_probes_withshifting.bed \
output/stats.rmd
Output is here: output/stats.md