Charity Z Goeckeritz
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Activity overview
Latest activity by Charity Z Goeckeritz-
Charity Z Goeckeritz commented,
Hi Gökalp, Thanks for your quick response! This issue is for GenotypeGVCFs - is that what you mean? I guess, either way, my problem still stands. GenomicsDBImport was also giving me the same issue...
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Charity Z Goeckeritz created a post,
genotypeGVCFs won't use more than 2G no matter how much memory I give it...
Hi there, I am using GATK version 4.0.11.0 (kind of outdated, I know...) but I'm experiencing a weird issue I'm not sure is version specific. No matter what I do, I can't seem to get GenotypeGVCFs ...
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Charity Z Goeckeritz commented,
Hi Gökalp, Yes, that makes sense! Thank you!
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Charity Z Goeckeritz commented,
Was it ever clarified why HaplotypeCaller didn't seem to be using the multiple cores it was provided? Is that something you have to explicitly ask for somehow aside from the --native-pair-hmm-threa...
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Charity Z Goeckeritz commented,
Hi Gökalp Çelik,Thanks so much for your reply. I can ask our admin to install the latest version but I've already run HaplotypeCaller with the present version, which took me several days... so I he...
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Charity Z Goeckeritz created a post,
GenomicsDBImport only going through the first chromosome when given a list
Hi there, I am using GATK v4.0.11.0 and having an issue with GenomicsDBImport. I've tried giving it intervals in the actual command and as a list so that I can make a database for my entire genome,...