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ensembl-gh-mirror
ensembl-rest
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!144
remove ExAC plugin docs, add refseq and merged opts
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remove ExAC plugin docs, add refseq and merged opts
github/fork/willmclaren/master
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master
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Marek Szuba
requested to merge
github/fork/willmclaren/master
into
master
8 years ago
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Created by: willmclaren
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master
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48685b7e
1 commit,
5 years ago
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root/documentation/vep.conf
+
10
−
5
Options
@@ -63,6 +63,16 @@
description
=
Include
aligned
RefSeq
mRNA
identifiers
for
transcript
.
NB
:
theRefSeq
and
Ensembl
transcripts
aligned
in
this
way
MAY
NOT
,
AND
FREQUENTLY
WILL
NOT
,
match
exactly
in
sequence
,
exon
structure
and
protein
product
default
=
0
</
xref_refseq
>
<
refseq
>
type
=
Boolean
description
=
Use
RefSeq
transcript
set
to
report
consequences
(
human
only
)
default
=
0
</
refseq
>
<
merged
>
type
=
Boolean
description
=
Use
merged
Ensembl
and
RefSeq
transcript
set
to
report
consequences
(
human
only
)
default
=
0
</
merged
>
<
Blosum62
>
type
=
Boolean
description
=
Include
BLOSUM62
amino
acid
conservation
score
(<
a
target
=
"_blank"
href
=
"https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/master/Blosum62.pm"
>
plugin
details
</
a
>)
@@ -89,11 +99,6 @@
description
=
Predictions
for
splicing
variants
from
dbscSNV
. (<
a
target
=
"_blank"
href
=
"https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/master/dbscSNV.pm"
>
plugin
details
</
a
>)
default
=
0
</
dbscSNV
>
<
ExAC
>
type
=
Boolean
description
=
Reports
allele
frequencies
from
the
Exome
Aggregation
Consortium
(<
a
target
=
"_blank"
href
=
"https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/master/ExAC.pm"
>
plugin
details
</
a
>)
default
=
0
</
ExAC
>
<
GeneSplicer
>
type
=
Boolean
description
=
Detects
splice
sites
in
genomic
DNA
(<
a
target
=
"_blank"
href
=
"https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/master/GeneSplicer.pm"
>
plugin
details
</
a
>)