Snakemake workflow: pdx-exome
This is a Snakemake workflow for generating variant calls from xenograft exome sequencing data (or similar targeted DNA-sequencing data from xenograft samples). The workflow is designed to handle paired-end (and optionally multi-lane) sequencing data.
The workflow essentially performs the following steps:
- The input reads are trimmed to remove adapters and/or poor quality base calls using cutadapt.
- The trimmed reads are aligned to the reference genome using bwa mem. The alignments are sorted by queryname using samtools.
- NGS-disambiguate is used to separate separate graft/host reads.
- The filtered graft bam file is coordinate-sorted using sambamba.
- Bam files from multiple lanes are merged using picard MergeSamFiles.
- Picard MarkDuplicates is used to remove optical/PCR duplicates.
- Variant calls are generated using freebayes.
QC statistics are generated using fastqc and samtools stats, and are summarized using multiqc.
Note that this workflow is still under active development.
Usage
Step 1: Install workflow
If you simply want to use this workflow, download and extract the latest release. If you intend to modify and further develop this workflow, fork this repository. Please consider providing any generally applicable modifications via a pull request.
In any case, if you use this workflow in a paper, don't forget to give credits to the authors by citing the URL of this repository and, if available, its DOI (see above).
Step 2: Configure workflow
Configure the workflow according to your needs by editing the config file
config.yaml and the samples file samples.tsv.
Step 3: Execute workflow
Test your configuration by performing a dry-run using
snakemake -n
Execute the workflow locally using
snakemake --cores $N
using $N cores or run it in a cluster environment using
snakemake --cluster qsub --jobs 100
or
snakemake --drmaa --jobs 100
See the Snakemake documentation for further details.
Authors
- Julian de Ruiter (@jrderuiter)