<s>
PLINK	B-Application
is	O
a	O
free	O
,	O
commonly	O
used	O
,	O
open-source	O
whole-genome	O
association	O
analysis	O
toolset	O
designed	O
by	O
Shaun	O
Purcell	O
.	O
</s>
<s>
PLINK	B-Application
currently	O
supports	O
following	O
functionalities	O
:	O
</s>
<s>
population	O
stratification	O
,	O
such	O
as	O
a	O
Principal	B-Application
component	I-Application
analysis	I-Application
;	O
</s>
<s>
PLINK	B-Application
has	O
its	O
own	O
format	O
of	O
text	O
files	O
(	O
.ped	O
)	O
and	O
binary	O
text	O
files	O
(	O
.bed	O
)	O
that	O
serve	O
as	O
input	O
files	O
for	O
most	O
analyses	O
.	O
</s>
<s>
Additionally	O
,	O
PLINK	B-Application
accepts	O
inputs	O
of	O
VCF	O
,	O
BCF	O
,	O
Oxford	O
,	O
and	O
23andMe	O
files	O
,	O
which	O
are	O
typically	O
extracted	O
into	O
the	O
binary	O
.bed	O
format	O
prior	O
to	O
performing	O
desired	O
analyses	O
.	O
</s>
<s>
PLINK	B-Application
has	O
a	O
variety	O
of	O
output	O
files	O
depending	O
on	O
the	O
analysis	O
.	O
</s>
<s>
PLINK	B-Application
has	O
the	O
ability	O
to	O
output	O
files	O
for	O
BEAGLE	O
and	O
can	O
recode	O
a	O
.bed	O
file	O
into	O
a	O
VCF	O
for	O
analyses	O
in	O
other	O
programs	O
.	O
</s>
<s>
Additionally	O
,	O
PLINK	B-Application
is	O
designed	O
to	O
work	O
in	O
conjunction	O
with	O
R	B-Language
,	O
and	O
can	O
output	O
files	O
to	O
be	O
processed	O
by	O
certain	O
R	B-Language
packages	O
.	O
</s>
<s>
PLINK	B-Application
2.0	O
a	O
comprehensive	O
update	O
to	O
PLINK	B-Application
,	O
developed	O
by	O
Christopher	O
Chang	O
,	O
with	O
the	O
improved	O
speed	O
of	O
various	O
Genome-wide	O
association	O
(	O
GWA	O
)	O
calculations	O
,	O
including	O
identity-by-state	O
(	O
IBS	O
)	O
matrix	O
calculation	O
,	O
LD-based	O
pruning	O
and	O
association	O
analysis	O
.	O
</s>
<s>
PLINK/SEQ	O
is	O
an	O
open-source	O
C/C	O
++	O
library	O
designed	O
for	O
analyzing	O
large	O
scale	O
whole-genome	O
and	O
whole-exome	O
studies	O
.	O
</s>
<s>
MQFAM	O
is	O
a	O
multivariate	O
test	O
of	O
association	O
(	O
MQFAM	O
)	O
that	O
can	O
be	O
efficiently	O
applied	O
to	O
large	O
population-based	O
samples	O
and	O
is	O
implemented	O
in	O
PLINK	B-Application
.	O
</s>
