Download PLINK - Psychiatric & Neurodevelopmental Genetics Unit (PNGU)

PHE
CHR
BP1
BP2
TYPE
KB
OLAP
OLAP U
OLAP R
Phenotype
Chromosome code
Start position (base-pair)
Stop position (base-pair)
DELetion or DUPlication
Kilobase length of CNV
Overlap (extent of CNV covered by gene)
Union overlap (ration of intersection to union)
Region overlap (extent of gene covered by CNV)
that might contain something like the following report
RANGE (+/FID
P001
P002
P003
P004
RANGE (+/FID
P001
P002
P003
P004
20kb ) [ 1 924206 925333 HES4 ]
IID
PHE CHR
BP1
BP2
1
2
1
789258 1232396
1
1
1
826576 1304312
1
2
1
864765 1913364
1
1
1
890974 1258710
20kb ) [ 1 938709 939782 ISG15 ]
IID
PHE CHR
BP1
BP2
1
2
1
789258 1232396
1
1
1
826576 1304312
1
2
1
864765 1913364
1
1
1
890974 1258710
TYPE
DUP
DEL
DUP
DUP
KB
443.1
477.7
1049
367.7
OLAP
0.09281
0.08609
0.03922
0.1118
OLAP U
0.09281
0.08609
0.03922
0.1118
OLAP R
1
1
1
1
TYPE
DUP
DEL
DUP
DUP
KB
443.1
477.7
1049
367.7
OLAP
0.09269
0.08598
0.03917
0.1117
OLAP U
0.09269
0.08598
0.03917
0.1117
OLAP R
1
1
1
1
That is, this is a list of any CNV that at least partially overlaps these two genes. The exact behavior can
be modified with flags such as --cnv-del, --cnv-kb, --cnv-disrupt, --cnv-overlap, --filter-cases,
etc.
27.14
Reporting sets of overlapping segmental CNVs
Finally, there are two option to group or report sets of segments that span a particular position. In the first
case, use the option
--segment-group
which takes all segments in a given region (whole genome unless otherwise specified) and forms ”pools”
of overlapping segments. Several pools of overlapping segments will be created; these will be listed in order
of decreasing size (number of segments); note that the same segment can appear in multiple pools (e.g. if
A overlaps with C, and B overlaps with C, but A and B do not overlap). The pools give information as
described below.
The more restricted form of this command forms a single pool of all segments that overlap a particular
position, which takes a single parameter of a marker name; typically these will be the dummy pos* markers
created by the --cnv-make-map command.
--segment-spanning pos119
In this case, for some made-up data, we see from the plink.cnv.summary file that there are 8 cases and
6 controls with a segment spanning a particular position, pos586
CHR
...
1
...
SNP
...
pos586
...
BP
...
16631570
...
AFF
...
8
...
UNAFF
...
6
...
In this case, there is unsurprisingly no association between segmental CNVs and disease: for example,
the corresponding position in the plink.cnv.summary.mperm file shows an empirical p-value of 0.35, but of
p=1 if adjusted for multiple testing (EMP2)
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