Eric C. Anderson
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Activity overview
Latest activity by Eric C. Anderson-
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...