James Santangelo

icon indicating a website link https://james-s-santangelo.github.io/ icon indicating an email [email protected]

icon location Berkeley, CA icon location Miller Postdoctoral Fellow in Rasmus Nielsen's lab in the Department of Integrative Biology at UC Berkeley

Results 6 comments of James Santangelo

The format of gdistkey file?

Hey all, I ran into the same issue. It looks like gdistkey is set to `None` when the VCF is loaded, regardless of what key is passed. In other words,...

LDhat Error in locs file: SNPs must be montonically increasing

This error is occurring because the site positions in the *.locs* file are not ordered. You can fix this error by making sure the initial VCF processed by `vcftools` is...

Switch from Travis CI to GitHub Actions

Damn, I think I had heard about some stuff going on over at Travis-CI but didn't realize it was this crazy. I'm happy to help migrate over to GitHub Actions....

ERROR The following inds are not in vcfR object

Sure thing! I've attached the popmap and VCF (`tmp.txt` -- renamed since GitHub didn't like the VCF extension). Here is the code I was using: ``` library(vcfR) library(GenotypePlot) library(tidyverse) vcf

ERROR The following inds are not in vcfR object

Yup, added in above message, thanks! The `test` object was just part of my unsuccessful attempt to troubleshoot. James

ERROR The following inds are not in vcfR object

Awesome, thanks for sorting this out so quickly, Jim! James