I use the snp array data to call the copy number variants. Then, I convert CNV to plink format, namely, .cnv .map .fam. But, I was very confused about the .map file, e.g. 1 p1-723307 0 723307
1 p1-752721 0 752721
1 p1-767096 0 767096
1 p1-779322 0 779322
1 p1-779323 0 779323
1 p1-801536 0 801536
- How it was derived from .cnv file? and what is the role of .map file?
** When I analyze the CNV burden, the results as
TEST GRP AFF UNAFF N ALL 38228 855932 RATE ALL 2.671 2.637 PROP ALL 1 1 TOTKB ALL 545.8 521.3 AVGKB ALL 205.9 198.5
with the parametere meaning:
RATE: Number of segments PROP: Proportion of sample with one or more segment TOTKB: Total kb length spanned AVGKB: Average segment size
I find the AVGKB is not equal to the average size of my CNV. **
- So, what is the meaning of segment?
Any opinion will be appreciated!