<s>
SnpEff	B-Application
is	O
an	O
open	O
source	O
tool	O
that	O
annotates	O
variants	O
and	O
predicts	O
their	O
effects	O
on	O
genes	O
by	O
using	O
an	O
interval	O
forest	O
approach	O
.	O
</s>
<s>
SnpEff	B-Application
has	O
been	O
used	O
for	O
various	O
applications	O
–	O
from	O
personalized	O
medicine	O
at	O
Stanford	O
University	O
,	O
to	O
profiling	O
bacteria	O
.	O
</s>
<s>
SnpEff	B-Application
has	O
the	O
capability	O
to	O
work	O
on	O
Windows	O
,	O
Unix	O
or	O
Mac	O
systems	O
,	O
although	O
the	O
installation	O
steps	O
differ	O
.	O
</s>
<s>
For	O
all	O
systems	O
,	O
SnpEff	B-Application
is	O
first	O
downloaded	O
as	O
a	O
ZIP	O
file	O
,	O
decompressed	O
and	O
then	O
copy-pasted	O
into	O
the	O
desired	O
software	O
(	O
Windows	O
)	O
or	O
requires	O
an	O
additional	O
command	O
line	O
(	O
Unix	O
and	O
Mac	O
)	O
.	O
</s>
<s>
Once	O
the	O
software	O
is	O
installed	O
,	O
the	O
user	O
inputs	O
a	O
VCF	O
or	O
TXT	B-General_Concept
file	I-General_Concept
into	O
the	O
tool	O
kit	O
that	O
contains	O
the	O
tab-separated	O
columns	O
:	O
Chromosome	O
name	O
,	O
Position	O
,	O
Variant	O
’s	O
ID	O
,	O
Reference	O
genome	O
,	O
Alternative	O
,	O
Quality	O
score	O
,	O
Quality	O
filter	O
and	O
Information	O
.	O
</s>
<s>
Any	O
other	O
genomic	O
information	O
is	O
put	O
in	O
the	O
INFO	O
column	O
,	O
which	O
is	O
altered	O
to	O
display	O
the	O
output	O
after	O
running	O
SnpEff	B-Application
.	O
</s>
<s>
The	O
Effect	O
impact	O
is	O
what	O
SnpEff	B-Application
uses	O
to	O
determine	O
how	O
deleterious	O
the	O
variant	O
is	O
on	O
genes	O
.	O
</s>
<s>
For	O
example	O
,	O
a	O
HIGH	O
impact	O
output	O
means	O
that	O
SnpEff	B-Application
predicts	O
that	O
the	O
variant	O
causes	O
deleterious	O
gene	O
effects	O
.	O
</s>
<s>
SnpEff	B-Application
is	O
typically	O
used	O
for	O
research	O
and	O
academic	O
purposes	O
at	O
institutions	O
and	O
companies	O
-	O
and	O
in	O
some	O
instances	O
,	O
personalized	O
medicine	O
.	O
</s>
<s>
However	O
,	O
Pablo	O
Cingolani	O
now	O
recommends	O
that	O
ClinEff	O
(	O
a	O
combination	O
of	O
SnpEff	B-Application
and	O
SnpSift	O
)	O
be	O
used	O
for	O
medical	O
purposes	O
.	O
</s>
<s>
SnpEff	B-Application
Advantages	O
:	O
</s>
<s>
SnpEff	B-Application
Limitations	O
:	O
</s>
<s>
SnpEff	B-Application
was	O
last	O
updated	O
in	O
January	O
2022	O
.	O
</s>
