Jeff Hammerbacher
Jeff Hammerbacher
Cf. https://github.com/igvteam/igv.js/issues/222
@rleonid could you say more about what you're tracking with this issue?
Also any transplant or personalized neoantigen vaccine data sets would be good
Might be some interesting data in [Human leukocyte antigen typing using a knowledge base coupled with a high-throughput oligonucleotide probe array analysis](https://www.ncbi.nlm.nih.gov/pubmed/25505899?dopt=Abstract) (2014), also available on ImmPort: http://www.immport.org/immport-open/public/study/study/displayStudyDetail/SDY422.
From Bobby Sebra in relation to getting PacBio data: >We now regularly run the PacBio HLA protocol for about the past 9 months so this isn’t hard to do, especially...
May also want to consider https://sites.google.com/site/bioericscript as it's what UCSC's ProTECT uses for fusion calling in their neoepitope selection pipeline.
Grab a `highmem` type! https://cloud.google.com/compute/docs/machine-types
@smondet what is this blocked on?
@smondet sounds like we're not blocked then, we should implement the self-hosting workaround.
`gs://genomics-public-data` has FASTAs, we'll need to build our own indexes