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Klinische Genetica
capture-lumc
vtools
Commits
e6309163
Commit
e6309163
authored
Nov 25, 2019
by
van den Berg
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The discordant VCF file is gzipped
parent
e62c9164
Pipeline
#2865
failed with stage
in 21 seconds
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README.md
README.md
+1
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vtools/cli.py
vtools/cli.py
+1
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README.md
View file @
e6309163
...
...
@@ -159,7 +159,7 @@ Options:
-ps
,
--positive-samples
TEXT Sample
(
s
)
in
positive-vcf to consider. May be
called multiple
times
[
required]
-s
,
--stats
PATH Path to output stats json file
-dc
,
--discordant
PATH Path to output
discordant VCF
file
-dc
,
--discordant
PATH Path to output
gzipped discordant vcf
file
-mq
,
--min-qual
FLOAT Minimum quality of variants to consider
-md
,
--min-depth
INTEGER Minimum depth of variants to consider
--help
Show this message and exit.
...
...
vtools/cli.py
View file @
e6309163
...
...
@@ -35,7 +35,7 @@ from .gcoverage import RefRecord, region_coverages
@
click
.
option
(
"-s"
,
"--stats"
,
type
=
click
.
Path
(
writable
=
True
),
help
=
"Path to output stats json file"
)
@
click
.
option
(
"-dvcf"
,
"--discordant-vcf"
,
type
=
click
.
Path
(
writable
=
True
),
help
=
"Path to output
discordant VCF
file"
,
help
=
"Path to output
gzipped discordant vcf
file"
,
required
=
False
)
@
click
.
option
(
"-mq"
,
"--min-qual"
,
type
=
float
,
help
=
"Minimum quality of variants to consider"
,
default
=
30
)
...
...
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