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Ok, it looks like it was the MQ filter that was causing the headache. I removed it and it seems to work now.
Hi Geraldine, Do you think it's a problem with how I created the gvcf files, or some problem with the options I'm passing to the VariantRecalibrator? Thanks, Adam
Thanks, Geraldine. Much appreciated!
Hi Geraldine, Any luck with the files? I'm hoping it's just a minor bug on my end that's preventing VariantRecalibrator from working properly, but I haven't managed to figure it out. Thanks, Adam
Thanks, Geraldine. I've run a few tests and can confirm that no matter what subset of gVCF files I use, the downstream VariantRecalibrator step fails. I just uploaded the reference, the raw vcf file for one of the runs, and the sites file (along wit…
Thanks, Geraldine. Below are the commands I used for the GVCF genotyping and variant recalibration (minus ~80 --variant lines; yes, I realize I should make a list of GVCF files as pass that as a single command line argument). From what I can tell, t…