Snakemake-cnvseq is a snakemake workflow that generates copy number profiles/calls from CNV-seq (shallow whole genome sequencing) data. The workflow is designed to handle single-end and (optionally) multi-lane sequencing data. The actual copy number profiles and calls are generated using the QDNAseq R package.
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 its DOI (see above).
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 aln. (Bwa aln is used because we typically have data with short read lengths. Bwa mem support can be added on request.)
- The alignments are sorted and indexed using samtools.
- Bam files from multiple lanes are merged using samtools.
- Picard MarkDuplicates is used to remove optical/PCR duplicates.
- The final alignments are indexed using samtools index.
- QDNAseq is used to generate copy number profiles/calls from the alignments. This step also supports optional normalization using normal samples and blacklisting of specific genomic regions.
QC statistics are generated using fastqc, samtools stats and picard MarkDuplicates. The stats are summarized into a single report using multiqc.
Alogether, this results in the following dependency graph:
Note that the QDNAseq step should be configured carefully to reflect the used
genome and read length. Make sure that a bin annotation is available for your
reference genome and read length, otherwise you may need to generate one.
(See the QDNAseq documentation for more details.) Alternatively, if no
bin annotation is available for your specific read length, you can also trim
your reads to a supported length in the cutadapt step.
Documentation is available at http://jrderuiter.github.io/snakemake-cnvseq
This software is released under the MIT license.