The main output file is DATA.xcnv, which contains one line for each CNV called in an individual. The columns in this file denote the following quantities for that CNV, which are defined as in our previous paper (Fromer et al. 2012):

SAMPLE	sample name in which CNV was called
CNV	type of copy number variation (DEL or DUP)
INTERVAL	genomic range of the called CNV
KB	length in kilobases of called CNV
CHR	chromosome name on which CNV falls
MID_BP	the midpoint of the CNV (to have one genomic number for plotting a single point, if desired)
TARGETS	the range of the target indices over which the CNV is called (NOTE: considering only the FINAL set of post-filtering targets)
NUM_TARG	# of exome targets of the CNV
Q_EXACT	Phred-scaled quality of the exact CNV event along the entire interval - Identical to EQ in .vcf output from genotyping
Q_SOME	Phred-scaled quality of some CNV event in the interval - Identical to SQ in .vcf output from genotyping
Q_NON_DIPLOID	Phred-scaled quality of not being diploid, i.e., DEL or DUP event in the interval - Identical to NDQ in .vcf output from genotyping
Q_START	Phred-scaled quality of “left” breakpoint of CNV - Identical to LQ in .vcf output from genotyping
Q_STOP	Phred-scaled quality of ‘right” breakpoint of CNV - Identical to RQ in .vcf output from genotyping
MEAN_RD	Mean normalized read depth (z-score) over interval - Identical to RD in .vcf output from genotyping
MEAN_ORIG_RD	Mean read depth (# of reads) over interval - Identical to ORD in .vcf output from genotyping