I ran BCBio's variant2 pipeline on 10 input (sorted) bams (via a slightly modified gatk-variant.yaml config file) and am trying to obtain a combined callable regions file across all of the samples. So far, I have several BED files generated per sample, but at what point will the globally shared callable regions BED file be generated?
I see that there's a function called
callable.py- is this where the globally shared callable regions file gets produced? If so, at what point in the pipeline does it get implemented or what YAML config details do I need to add for it to occur?
yaml config file:
--- details: - analysis: variant2 genome_build: hg38 # to do multi-sample variant calling, assign samples the same metadata / batch # metadata: # batch: your-arbitrary-batch-name algorithm: aligner: false bam_clean: fixrg mark_duplicates: true recalibrate: false variantcaller: false nomap_split_size: 250 #this is the default number of unmapped base pairs nomap_split_targets: 200 #this is the default number of target intervals # for targetted projects, set the region # variant_regions: /path/to/your.bed