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I am using UG to call both SNP and INDELS across 179 different samples for RAD sequencing. I keep getting this error:
The odd thing is while it repeatedly happens, it never throws the exact same error. It's always at a different place in the alignment. I tried rerunning the whole pipeline with the 8/16 nightly build (including reduce reads) and it is still doing this. I've tried with and without using a BED interval file as well.
Is there any way to get GATK to just not output a call and keep going?