This tool takes as input a table on binned read counts (from Define CNA-seq experiment), and filters out bins that are known to behave spuriously.
By default, bins in the QDNAseq or ENCODE blacklists are filtered out, as are the sex chromosomes. A minimum mappability can also be specified.
Data table with the chosen bins filtered out.
Scheinin et al. (2014) DNA copy number analysis of fresh and formalin-fixed specimens by whole-genome sequencing: improved correction of systematic biases and exclusion of problematic regions. Manuscript submitted.
Mappability: Koehler et al. (2011) The uniqueome: a mappability resource for short-tag sequencing. Bioinformatics 27: 272-274