A nextflow (Di Tommaso, 2017) pipeline implementing the Strelka2 (Kim, 2017) pipeline for somatic variant calling of tumor-normal pairs.
$ nextflow run tron-bioinformatics/tronflow-strelka2 -profile conda --help
Usage:
nextflow run tron-bioinformatics/tronflow-strelka2 -profile conda --input_files input_files --reference reference.fasta
Input:
* input_files: the path to a tab-separated values file containing in each row the sample name, tumor bam and normal bam
The input file does not have header!
Example input file:
name1 tumor_bam1 normal_bam1
name2 tumor_bam2 normal_bam2
* reference: path to the FASTA genome reference (indexes expected *.fai)
Optional input:
* output: the folder where to publish output
* intervals: path to the BED file containing genomic intervals. Will assume WGS if not given
* memory: the ammount of memory used by each job (default: 16g)
* cpus: the number of CPUs used by each job (default: 2)
Output:
* Final somatic calls VCF
The input table expects three tab-separated columns without a header. Replicate BAM files can be provided comma-separated, this will be merged into a single BAM file.
| Patient name | Tumor BAMs | Normal BAMs |
|---|---|---|
| patient_1 | /path/to/patient_1.tumor.bam | /path/to/patient_1.normal.bam |
| patient_2 | /path/to/patient_2.tumor.1.bam,/path/to/patient_2.tumor.2.bam | /path/to/patient_2.normal.1.bam,/path/to/patient_2.tumor.2.bam |
If replicates are provided, a conservative approach would be filter out variants not detected in every pairwise combination. A more relaxed approach would the opposite to keep them all. At the moment we just merge all reads in a single BAM, thus we lose the advantage of having replicates apart from having greater coverage.
The Strelka2 germline pipeline is not implemented.
- Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., & Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature Biotechnology, 35(4), 316–319. https://doi.org/10.1038/nbt.3820
- Kim, S., Scheffler, K., Halpern, A. L., Bekritsky, M. A., Noh, E., Källberg, M., Chen, X., Beyter, D., Krusche, P., & Saunders, C. T. (2017). Strelka2: Fast and accurate variant calling for clinical sequencing applications. BioRxiv, 192872. https://doi.org/10.1101/192872