Snakemake workflow to process WGS trio data from MGI instrument
To run this analysis, a couple of dependencies need to be met:
- parabricks ≥ v3.2.0.1
- python ≥ 3.8
- snakemake ≥ 5.22.1
- Singularity ≥ 3.7
We are using resources from Broad Institute:
Homo_sapiens_assembly38.fasta+ bwa index, faidx and dict- bgzipped version of
Homo_sapiens_assembly38.dbsnp138.vcf+ tabix Homo_sapiens_assembly38.known_indels.vcf.gz+ tabix
The workflow may be started doing something like this:
snakemake \
-s Snakefile \
--use-singularity \
--singularity-args " --cleanenv --bind /Path/to/data/and/references"
Make sure to add the desired file paths to config.yaml, sample.tsv, units.tsv and pedigree.tsv.