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Germline short variant discovery with GATK4, exome sequencing, single sample
Dear GATK team,
I'm implementing "Germline short variant discovery" (we often do not have matched normal samples, otherwise I'd go for the somatic pipeline) with GATK4. We do exome sequencing and we generally look at only 1 or a couple of samples at a time.
Thus the following sentence in joint-discovery-gatk4-local.wdl has me a bit concerned:
## - Bare minimum 1 WGS sample or 30 Exome samples. Gene panels are not supported.
How hard is this requirement for 30 samples minimum and what step exactly requires it? What would you recommend if I just have a single BAM file from a single exome sequenced patient/sample, made using processing-for-variant-discovery-gatk4.wdl?