Derek Caetano-Anolles
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Recent activity by Derek Caetano-Anolles Sort by recent activity-
Good question, Bhoom Suktitipat. Unfortunately, the date on that article is not accurate. Maybe someone else on the GATK team made an update? I've updated the article to list out the relevant dates...
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I'm sorry that you feel that way. The tone of the article was intended to make a technical topic more engaging and draw attention to a change that might otherwise be overlooked in the release notes...
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Sorry, I can't see another post. Your profile says you've only posted this one ¯\_(ツ)_/¯ Anyway, it's totally fine to question the decision to change the output format... it's also why we reverted ...
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Hi Eva (Evander) -- Good question. The variant calls were not made in the alt contig region, but were based on the Illumina masked reference available in the following DRAGEN-reference in the GCP ...
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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...
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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...
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Felipe Batalini Good catch. The video link has been updated. Thanks for bringing it to my attention!
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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.
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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...
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Hi again Takeshi Yoshimura, Thanks for the recommendation! I've just updated the document now.