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DPclust-nf

Nextflow pipelines to run DPclust on sequencing data

Description

Nextflow pipeline to run tumor subclone detection software DPclust, perform postprocessing and run mutationTimeR to date amplifications

Dependencies

  1. This pipeline is based on nextflow. As we have several nextflow pipelines, we have centralized the common information in the IARC-nf repository. Please read it carefully as it contains essential information for the installation, basic usage and configuration of nextflow and our pipelines.
  2. External software:
  • DPclust. R package to cluster mutations to detect tumor subclones
  • dpclust3p. R package with useful functions to format DPclust inputs
  • MutationTimeR. R package to time amplification events

Input

Type Description
CNV_file Path to tab-separated file with copy number variants for all samples, in PURPLE format (see e.g. our purple-nf pipeline)
CNV_summary_file Path to tab-separated file with copy number summary for all samples (in PURPLE output format)
input_file Path to Input file (tab-separated values) with 4 columns: sampleID, vcf, normal, and tumor

Parameters

  • Optional

Name Default value Description
--vcf_folder . Path to folder with variants for all samples in VCF format
--bam_folder . Path to folder with BAM/CRAM files for tumor and normal samples
--output_folder . Path to output folder
--cpu 2 Number of cpus used
--mem 8 Memory used in Gb
--ext cram Extension of alignment files, cram or bam

  • Flags

Flags are special parameters without value.

Name Description
--help Display help

Usage

nextflow run iarcbioinfo/DPclust-nf [-with-docker] [OPTIONS]

Output

Type Description
DPclust_inputs Folder with inputs to DPclust formatted using dpclust3p: a folder for each sample with a DPmasterfile summarizing the files necessary to run DPclust, formatted CNVs and allele frequency tables
results/DPclust Folder with outputs from DPclust: a folder for each sample with the location (CCF and number of alterations) of each subclone
results/MutationTimeR Folder with results from mutationtimeR: timing of CNVs and SNVs

Contributions

Name Email Description
Nicolas Alcala* [email protected] Developer to contact for support