Can you please provide
a) GATK version used
b) Exact GATK commands used
c) The entire error log if applicable.
I am trying to perform mutation calling on 50 6-8X whole genomes corresponding to subclones derived from a parental cell line with a 30X WGS. I am interested in identifying ALL variants across the cohort of lower coverage whole genomes that are not present in the parental line (including cases with alt count of 1 or where there is low depth in my normal).
What would be the best set of settings to use for this analysis? I could imaging performing joint calling with all 50 clones using the same matched normal with the following settings:
and then removing variants that are also in the normal, but suspect there is a more efficient way to implement the caller. Any further suggestions welcome!
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