Within Illumina's Basespace you can only do variant calling on up to 96 samples at any one time using the app BWA Enrichment - so you'd have to do batch calling for a larger cohort. Is joint calling a vital step when your cohort is <200 samples? I know ideally joint calling would be performed for a greater sensitivity for low-frequency variants - but is this only the case for when the coverage is low for a certain gene region?
I see it recommended here to do joint calling, but I get the impression that is for when large numbers of samples are involved.
Thanks a million!