anitalu724 / VCFMAF

tags: Lab

MutScape

MutScape is a Python tool for preprocessing variant call format(VCF) and mutation annotation format(MAF) files and

Prerequisite

pip install termcolor
pip install tqdm
pip install numpy
pip install pandas
pip install vcfpy
pip install seaborn
pip install oncodriveclust
pip install comut

---

Preprocessing VCF files and MAF files

python3 vcf_maf_process.py ...

Required input files(Required)

python3 vcf_maf_process.py \
-f [tsv file path]

• for VCF files: a 9 columns TSV file

NORMAL	TUMOR	MuSe	Mutect2	SomaticSniper	Strelka2	VarScan2	At Least # CALLS	At Most # REJECT
...	...	...	...	...	...	...	...	...

• for MAF files: a 1 column TSV file

MAF
...

For VCF preprocessing

VCF filtering

python3 vcf_maf_process.py \
...
-vf GI "[1:3,5]" CI "15,15,0,0,0,0.05,8,8" P 1 FFPE 0.9 \
...

VCF combination

python3 vcf_maf_process.py \
...
-c \
...

VCF transform to MAF

python3 vcf_maf_process.py \
...
-v2m 48 \
...

For MAF preprocessing

MAF filtering

python3 vcf_maf_process.py \
...
-mf GI "[1:3,5]"
...

Output files and Meta files

python3 vcf_maf_process.py \
...
-o [output files path] \
-m [meta files path] \
...

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Data Analysis and Visualization

CoMut Plot Analysis

Mutational Signature

1. Preprocessing: Make all MAFs into one MAF file

python3 vcf_maf_process.py \
-f examples/Tissue_samples/ms_maf/maf.tsv \
-m examples/Tissue_samples/ms_maf \
-o examples/Tissue_samples/ms_maf

2. Estimation

python3 maf_analysis.py \
-f examples/Tissue_samples/ms_maf/maf_combination.maf \
-ms 1 "[2,9,10]" \
-o examples/Tissue_samples/outputs \
-p examples/Tissue_samples/pictures

3. Analysis and Visualization

python3 maf_analysis.py \
-f examples/Tissue_samples/ms_maf/maf_combination.maf \
-ms 2 "[3]" \
-o examples/Tissue_samples/outputs \
-p examples/Tissue_samples/pictures

4. Outputs

HRD Score, Whole-Genome doubling(WGD) and Chromosome instability(CIN)

1. HRD Score

python3 maf_analysis.py \
-f examples/CBCP_samples/CBCP_oncokb_maf.txt \
-hrd examples/CBCP_samples/HRD_input.tsv grch37 \
-o examples/CBCP_samples/outputs \
-p examples/CBCP_samples/pictures

2. WGD_CIN

python3 maf_analysis.py \
-f examples/CBCP_samples/CBCP_oncokb_maf.txt \
-wgdcin examples/CBCP_samples/HRD_input.tsv \
-o examples/CBCP_samples/outputs \
-p examples/CBCP_samples/pictures

3. ONCOKB

python3 maf_analysis.py \
-f examples/TCGA/TCGA_Mutect_v10_white_rerun.maf \
-oncokb ../oncokb-annotator/ ca398551-c549-49bd-80f0-0e68d9ca033c 4 examples/TCGA/clinical_input.txt \
-o examples/TCGA/outputs \
-p examples/TCGA/pictures

4. Outputs examples

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