Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Set Tumor-Normal ratio cut-off to 0 #5

Open
wants to merge 5 commits into
base: master
Choose a base branch
from
Open

Set Tumor-Normal ratio cut-off to 0 #5

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
5 commits
Select commit Hold shift + click to select a range
e43f13b
Merge pull request #9 from rhshah/master
rhshah Jul 24, 2017
7e3da88
Set Tumor-Normal ratio to 0 in filter_mutect.py
nikhil Sep 15, 2017
c697fc4
Set Tumor-Normal ratio to 0 in filter_pindel.py
nikhil Sep 15, 2017
c420b05
Set Tumor-Normal ratio to 0 in filter_sid.py
nikhil Sep 15, 2017
8a8db3d
Set Tumor-Normal ratio to 0 in filter_vardict.py
nikhil Sep 15, 2017
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 1 addition & 1 deletion mutect/filter_mutect.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -44,7 +44,7 @@ def main():
parser.add_argument("-tsn", "--tsampleName", action="store", dest="tsampleName", required=True, type=str,metavar='SomeName', help="Name of the tumor Sample")
parser.add_argument("-dp", "--totaldepth", action="store", dest="dp", required=False, type=int, default=0, metavar='0', help="Tumor total depth threshold")
parser.add_argument("-ad", "--alleledepth", action="store", dest="ad", required=False, type=int, default=5, metavar='5', help="Tumor allele depth threshold")
parser.add_argument("-tnr", "--tnRatio", action="store", dest="tnr", required=False, type=int, default=5, metavar='5', help="Tumor-Normal variant frequency ratio threshold ")
parser.add_argument("-tnr", "--tnRatio", action="store", dest="tnr", required=False, type=int, default=0, metavar='0', help="Tumor-Normal variant frequency ratio threshold ")
parser.add_argument("-vf", "--variantfrequency", action="store", dest="vf", required=False, type=float, default=0.01, metavar='0.01', help="Tumor variant frequency threshold ")
parser.add_argument("-hvcf", "--hotspotVcf", action="store", dest="hotspotVcf", required=False, type=str, metavar='hostpot.vcf', help="Input bgzip / tabix indexed hotspot vcf file to used for filtering")
parser.add_argument("-o", "--outDir", action="store", dest="outdir", required=False, type=str, metavar='/somepath/output', help="Full Path to the output dir.")
Expand Down
4 changes: 2 additions & 2 deletions pindel/filter_pindel.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -87,8 +87,8 @@ def main():
dest="tnr",
required=False,
type=int,
default=5,
metavar='5',
default=0,
metavar='0',
help="Tumor-Normal variant frequency ratio threshold ")
parser.add_argument(
"-vf",
Expand Down
6 changes: 3 additions & 3 deletions somaticindeldetector/filter_sid.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -95,8 +95,8 @@ def main():
dest="tnr",
required=False,
type=int,
default=5,
metavar='5',
default=0,
metavar='0',
help="Tumor-Normal variant frequency ratio threshold ")
parser.add_argument(
"-vf",
Expand Down Expand Up @@ -245,4 +245,4 @@ def checkHotspot(hotspotVcf, chromosome, start):
end_time = time.time()
totaltime = end_time - start_time
logging.info("filter_sid: Elapsed time was %g seconds", totaltime)
sys.exit(0)
sys.exit(0)
4 changes: 2 additions & 2 deletions vardict/filter_vardict.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -86,8 +86,8 @@ def main():
dest="tnr",
required=False,
type=int,
default=5,
metavar='5',
default=0,
metavar='0',
help="Tumor-Normal variant frequency ratio threshold ")
parser.add_argument(
"-vf",
Expand Down