Powered by GitBook

1 of 1

Loading...

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

Creating this file might be a hassle. Helper script could possibly be made to help with this

Required Columns for maf file

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 )

Y

cna_path

cna file

Absolute file paths

sample level cna file ()

N

sv_path

sv file

Absolute file paths

<code></code>

N

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

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

helper script included