I've run germline WDL pipeline on 2838 individuals and hg38 assembly.
The code was taken from here:
and linked from here (The JointGenotyping workflow takes the GVCF output ...):
My final output contains 7094 files. Sharded VCF files are not merged back into a single VCF or chromosome-based VCFs. Is this normal and I need to merged it manually?
Also, I am confused which WDL should I use in future as Terra contains different and older code:
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