filter_gaps

[Pastellem]

Hello,

I'm using Lumpy, Breakseq, breakdancer, pindel and cnvnator to look for CNVs in fastq obtained by WES (I know it's not the most adaptable tools for WES).

I would like to know the impact of the --filter_gaps option on merging files? How does it work ?

[marghoob]

Hi @Pastellem, --filter_gaps will remove the calls overlapping with the N-regions in the reference genome sequence (hg38, b37). This will most commonly affect the calls made by CNV calling tools since they may infer the lack of coverage in N-regions as an evidence for deletions. Since these are false calls, we filter such calls out by overlapping the gaps BED file when this flag is used.