CNA-seq / Filter copy number bins

Description

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.

Parameters

Details

By default, bins in the QDNAseq or ENCODE blacklists are filtered out, as are the sex chromosomes. A minimum mappability can also be specified.

Output

Data table with the chosen bins filtered out.

References

QDNAseq:
Scheinin et al. (2014) DNA copy number analysis of fresh and formalin-fixed specimens by shallow whole-genome sequencing with identification and exclusion of problematic regions in the genome assembly. Genome Res In Press.

Mappability:
Koehler et al. (2011) The uniqueome: a mappability resource for short-tag sequencing. Bioinformatics 27: 272-274