This directory contains general filters that are strongly encouraged to be applied to all ancient samples:
- Coverage filter stratified by GC content
- minimum coverage 10 
- Heng Li's Mapability 35 (requiring all 35mers to be unique, i.e. map35_100) 
- MQ25 
- no tandem repeats (from UCSC tandem repeat finder track)
- no indels (removes indels called with GATK)

The bed files give positions that pass filters, i.e. they should be included in analyses.