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# Template for whole genome Illumina variant calling with FreeBayes
# This is a GATK-free pipeline without post-alignment BAM pre-processing
# (recalibration and realignment)
---
details:
- analysis: variant2
genome_build: GRCh37
# to do multi-sample variant calling, assign samples the same metadata / batch
# metadata:
# batch: your-arbitrary-batch-name
algorithm:
aligner: bwa
variantcaller: freebayes
# for targetted projects, set the region
# variant_regions: /path/to/your.bed