Eric C. Anderson
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Activity overview
Latest activity by Eric C. Anderson-
Eric C. Anderson commented,
Oh Dear! And so, in the third year from its untimely demise the dot rose from its grave to wreak vengeance upon all who doubted it. Yikes! I hope that isn't too much work for y'all, but it sounds ...
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Eric C. Anderson commented,
Thanks a lot Genevieve! That is a really helpful blog post. It's exciting to hear about all the backend changes and efficiency increases happening. Best regards, eric
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Eric C. Anderson commented,
I love the title! Thanks so much for this blog post. I think it will be valuable for people dealing with low-coverage WGS data.
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Eric C. Anderson commented,
Just answered my issue #1 (above) using a solution with bcftools. If anyone is wondering how to code genotypes with DP=0 as missing, an easy solution with the bcftools setGT plugin is: bcftools +s...
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Eric C. Anderson commented,
Thank you for looking into that Genevieve. I appreciate that. Moving forward with VCF files produced by GATK, it would not be hard for me to identify missing genotypes as those that have DP=0 or...
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Eric C. Anderson commented,
Hello, I wanted to also report that GATK 4.2.6.1 seems to only rarely designate genotypes as "missing" at an individual, even when there are no reads at the site in the individual. I have a small ...
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Eric C. Anderson commented,
I just wanted to chime in to say that I have had success running GenotypeGVCFs 4.2.4.0 on genomicsDBs from GenomicsDBImport 4.2.4.1. A long run across 34 chromosomes and 14 collections of scaffold...
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Eric C. Anderson commented,
Hi Genevieve, thank you for working on this. And thank you Andrius for posting the error. I have the same problem. It is not just associated with --all-sites. The error seems to occur when the num...