Setup for Running Analysis
Master reference file descriptions
Master reference file
An example of this file can be found in the data/ folder
For not required columns, leave the cell blank if you don't have the information
Column Names
Information Specified
Specified format (If any)
Notes
Required
cmo_patient_id
Patient ID
None
Results are presented per unique patient ID
Y
cmo_sample_id_plasma
Plasma Sample ID
None
Y
cmo_sample_id_normal
Buffy Coat Sample ID
None
N
bam_path_normal
Unfiltered buffy coat bam
Absolute file paths
N
paired
Whether the plasma has buffy coat
Paired/Unpaired
Y
sex
Sex
M/F
Unrequired
N
collection_date
Collection time points for graphing
dates (m/d/y)
OR
character strings (i.e. the sample IDs)
the format should be consistent within the file
Y
dmp_patient_id
DMP patient ID
*Patient IDs*
All DMP samples from this patient ID will be pulled
N
bam_path_plasma_duplex
Duplex bam
Absolute file paths
Y
bam_path_plasma_simplex
Simplex bam
Absolute file paths
Y
maf_path
maf file
Absolute file paths
Y
cna_path
cna file
Absolute file paths
N
sv_path
sv file
Absolute file paths
<code></code>
N
Creating this file might be a hassle. Helper script could possibly be made to help with this
Required Columns for maf file
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