How to remove CNV calls in immunoglobulin regions?
The CNV calls in immunoglobulin regions are most likely cell line artifact, so they should be removed as part of the QC procedure. The scan_region.pl program can be used to do this conveniently: scan_region.pl cnvcall imm_region -minqueryfrac 0.5 > cnvcall.imm fgrep -v -f cnvcall.imm cnvcall > cnvcall.clean This command first scan the cnvcall file against known immunoglobulin regions, and any CNV call that overlap with immunoglobulin regions are written to the cnvcall.imm file (the –minqueryfrac means that at least 50% of the length in the CNV call must overlap with the immunoglobulin region, to exclude cases where a very large CNV call happens to encompass the immunoglobulin regions). Then the fgrep program is used to remove these regions from the file and generate a cleaned cnvcall.clean file. The imm_region file contains immunoglobulin regions.
