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

• QDNAseq blacklist (remove, keep) [remove]
• ENCODE blacklist (remove, keep) [remove]
• minimum mappability (0-100) [0]

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