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	fillout_filtered.maf (required columns here)	Y
cna_path	cna file	Absolute file paths	sample level cna file (helper script included)	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

Hugo_Symbol,Chromosome,Start_Position,End_Position,Tumor_Sample_Barcode,Variant_Classification,HGVSp_Short,Reference_Allele,Tumor_Seq_Allele2,D_t_alt_count_fragment