Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

tabix.read remote files #20

Open
bschilder opened this issue Jul 25, 2021 · 3 comments
Open

tabix.read remote files #20

bschilder opened this issue Jul 25, 2021 · 3 comments

Comments

@bschilder
Copy link

Is it possible to query indexed VCF files that are stored remotely?

Thanks!

vcf_url <- "ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/release/20110521//ALL.chr18.phase1_release_v3.20101123.snps_indels_svs.genotypes.vcf.gz"

tab <- seqminer::tabix.read(tabixFile =vcf_url, tabixRange =  "8:48673708-48692728")
print(tab)

### character(0)
@bschilder
Copy link
Author

@zhanxw any news on this?

@bschilder
Copy link
Author

Hi @zhanxw, querying remote files would would be a really useful feature for seqminer to have. Any possibility this will be added?

@bschilder
Copy link
Author

@yang-lina perhaps you would be able to help with this?

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
1 participant
@bschilder