This directory contains indexed bam files for the ~28x coverage Chagyrskaya
Neandertal Genome generated from the Chagyrskaya 8 phalanx. The alignments were
produced by BWA (version: 0.5.10-evan.10, 
https://github.com/udo-stenzel/network-aware-bwa) against hg19 including the
1000 genomes decoy sequences (hs37d5), phi-X (NC_001422.1) and human
herpesvirus 4 type 1 (NC007605). 

This data was processed similar to previous archaic genomes: 
- Pairs with overlapping ends were merged into one sequence (leeHom)
- PCR duplicates were merged into one sequence based on their alignment
  coordinates (bam-rmdup 0.2).  This step keeps only aligned sequences that
  are properly paired or single reads.
- Indels were realigned with GATK (version 1.3.14)

The individual is female and the Y-chromosome alignments are only included for
completeness.

KP
pruefer@eva.mpg.de