`tabix.read` remote files

zhanxw / seqminer

Query sequence data (VCF/BCF1/BCF2, Tabix, BGEN, PLINK) in R

http://zhanxw.github.io/seqminer/

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`tabix.read` remote files #20

Open bschilder opened 3 years ago

bschilder commented 3 years ago

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 commented 2 years ago

@zhanxw any news on this?

bschilder commented 2 years ago

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

bschilder commented 2 years ago

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