You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
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 ?
The text was updated successfully, but these errors were encountered:
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.
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 ?
The text was updated successfully, but these errors were encountered: