MOTIVATION: High-throughput sequencing technologies enable the genome-wide 
analysis of the impact of genetic variation on molecular phenotypes at 
unprecedented resolution. However, although powerful, these technologies can 
also introduce unexpected artifacts.
RESULTS: We investigated the impact of library amplification bias on the 
identification of allele-specific (AS) molecular events from high-throughput 
sequencing data derived from chromatin immunoprecipitation assays (ChIP-seq). 
Putative AS DNA binding activity for RNA polymerase II was determined using 
ChIP-seq data derived from lymphoblastoid cell lines of two parent-daughter 
trios. We found that, at high-sequencing depth, many significant AS binding 
sites suffered from an amplification bias, as evidenced by a larger number of 
clonal reads representing one of the two alleles. To alleviate this bias, we 
devised an amplification bias detection strategy, which filters out sites with 
low read complexity and sites featuring a significant excess of clonal reads. 
This method will be useful for AS analyses involving ChIP-seq and other 
functional sequencing assays.
AVAILABILITY: The R package abs filter for library clonality simulations and 
detection of amplification-biased sites is available from 
http://updepla1srv1.epfl.ch/waszaks/absfilter