-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathargument_configs.tsv
We can make this file beautiful and searchable if this error is corrected: No tabs found in this TSV file in line 0.
60 lines (60 loc) · 2.14 KB
/
argument_configs.tsv
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
#lines beginning with pound are ignored
#this file is an example of arguments for the config tsv
#order doesnt matter, but you must include every possible argument even if it has no values
#
#path to bam file for input/proband
inputOrProbandBam
#
#path to fastq file for input/proband
inputOrProbandFastq
#
#path to vcf file for input/proband
inputOrProbandVcf /scratch/PI/euan/common/udn/gateway/data/UDN781395/747009-UDN781395-P_HLYC7BCXY-2-ID07.SNPs_Annotated.vcf
#
#tab delimited list of bam files for each family member
familyBams
#
#tab delimited list of fastq files for each family member
familyFastqs
#
#tab delimited list of vcf files for each family member
familyVcfs /home/noahfrie/common/udn/gateway/data/UDN100429/747010-UDN100429-D_HLYC7BCXY-2-ID09.SNPs_Annotated.vcf /home/noahfrie/common/udn/gateway/data/UDN862260/747365-UDN862260-M_HLYC7BCXY-2-ID08.SNPs_Annotated.vcf
#
#arguments for debugging (currently unimplemented)
debugArguments saveFiles
#
#calling--arguments for rtg (currently unimplemented)
calling rtg
#
#arguments for preprocessing. All valid options below
preprocessing smA chP rhP ccP rmD
#
#arguments for filtering. All valid options below
filtering fbL sgF
#
#path to list of variants to filter on for current case
variantListToFilterOn /home/noahfrie/noahfrie/devCode/stmp2/vcfanno/UDN781vars.txt
#
#arugments for annotation. All valid options below
annotation exA gnA clV
#
#arguments for web search annotations. All valid options below
websearchAnnotations omim rvis fathmm mTaster sift phylop mgi
#
#the udnid for the proband we are working with. Must be specified for powerpoint export to work
udnId UDN781395
#
#the path to the xls file created by the GCs in ingenuity
gcXls
#
#specify the path to an xls file that has already been generated by stmp if you would like to skip the earlier parts of the pipeline
alreadyGeneratedXls
#
#specify aspects of how pipeline will be run (slurm etc) currently unimplemented
runArchitecture
#
#path to relevant ped file (currently unimplemented)
pedFile
#
#final output directory for files
finalOutputDir /scratch/PI/euan/common/udn/gateway/data/UDN781395/