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CommentsRecent activity by Derek Caetano-Anolles Sort by recent activity
Thank you for your input, SAMUEL ANDREW ~ As you know, you can still determine the missing genotypes because the FORMAT DP will be 0 even within the current GenotypeGVCFs format. So it is still pos...
Eddy W - By default the VCF files will not recognize those variant sites as missing genotype. This would require converting the GenotypeGVCFs output to a format that PLINK will recognize, by replac...
Felipe Batalini Good catch. The video link has been updated. Thanks for bringing it to my attention!
Great! I'm glad it worked out. Don't hesitate to come back with more questions if you have GATK-related trouble further on down the line.
Hi samuel Welcome to using GATK! I hope that we can help get your pipeline sorted out and functioning. To start off with, your input command appears to be using `-conf` instead of the `--conf` opt...
Hi again Takeshi Yoshimura, Thanks for the recommendation! I've just updated the document now.
I agree, Eric C. Anderson! I think it's good to have this info accessible somewhere that Google (or our site's search bar) can easily find it. Also — thank you for inspiring this post with your com...
Hi Takeshi Yoshimura, I am the writer responsible for those documents. Thank you very much for your interest in helping us improve our documentation! Those two articles are actually in serious need...
It's pronounced GATK, using the same sound as in GIF. Hope that clears it up for you, Bob Chen!
Fantastic, I'm glad it was an easy fix. Best of luck with your project!