DEEPctMUT

DEEPctMUT is a Nextflow pipeline for highly accurate mutation detection in circulating tumor DNA (ctDNA) from plasma and optionally matchhed PBMC samples.

DEEPctMUT takes as input FASTQ files from paired-end sequencing with unique molecular barcode (UMI) of a plasma samples and optinaly matched PBMC samples. After candidate calling and multiple steps of error polishing DEEPctMUT outputs a VCF file with somatic mutations in ctDNA.

Dependeny

• nextflow >= 24.10.4
• miniconda >= 24.3.0

How to run

Test case

To test the pipeline on the provided toy dataset, download or git clone the repository and run the following command:

nextflow main.nf -profile conda,test --output_dir OUTUPUT_DIR

General case

To run DEEPctMUT on your own data, you need the hg19 reference genome indexed for BWA, as well as a dictionary file. You also need to prepare a single input_table, as csv file WITH header and formatted as follows:

patient	sample	Fastq1	Fastq2	type	replicate
Patient_1	Patient_1_plasma	/path/to/read1.fastq	/path/to/read2.fastq	Plasma	1
Patient_1	Patient_1_pbmc	/path/to/read1.fastq	/path/to/read2.fastq	PBMC	1

Then run the following command:

nextflow main.nf -profile conda --input_table INPUT_TABLE --reference REFERENCE --output_dir OUTUPUT_DIR

Arguments

The pipeline accepts the following command-line arguments:

Argument	Description	Required/Default
--input_table	CSV file with sample information.	Required unless -profile test
--output_dir	Output directory for results.	Required
--reference	hg19 Reference genome FASTA file. BWA index and dictionary files also need to be in the same directory.	Required
--bed_file	BED file with target regions.	Default: test_data/CRC_panel.bed
--with_pbmc	Whether to process PBMC samples for background filtering.	Default: true
--RF_threshold	Random Forest model threshold for variant calling.	Default: 0.21
--DeepES_threshold	DeepES model threshold to call a mutation significant.	Default: 0.01
--non_hotspot_reads	Minimum number of reads supporting a mutation on non-hostpot regions.	Default: 30
--min_vaf	Minimum variant allele frequency (VAF) to call a mutation.	Default: 0.0003

Output

DEEPctMUT outpus for each patient a VCF file with mutation calls in the specified output_dir directory.