This directory contains general filters that are strongly encouraged to be applied to Chagyrskaya:
- 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)

In addition to these filters, we also removed a total of 36 regions ranging
from 117 to 646 bp length in which we found alignments that contained a very
large proportion of mismatches. These alignments tend to mismatch for at least
50% of bases and are likely caused by a problem in the aligner.

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

Filters for other ancient genomes can be found here:
http://ftp.eva.mpg.de/neandertal/Vindija/FilterBed