README.md

In Bioconductor/Rhtsget: Interface to htsget retrieval from GA4GH

• specification: https://samtools.github.io/hts-specs/htsget.html
• python client: https://htsget.readthedocs.io/
• ga4gh news: https://www.ga4gh.org/news/-9msBlhISDK_ltjA7Vt6aA.article

Example

if (!"Rhtsget" %in% rownames(installed.packages()))
    BiocManager::install("Bioconductor/Rhtsget")
library(Rhtsget)
gr <- GenomicRanges::GRanges("chr12:111766922-111817529")
sample_id <- "platinum/NA12878"
endpoint <- "https://htsnexus.rnd.dnanex.us/v1"
fl <- tempfile(fileext=".bam")
bam <- htsget_reads(gr, sample_id, endpoint, fl)
Rsamtools::countBam(bam)

Two endpoints

• GET /reads/
• GET /variants/

Note from the specification:

We use the following pan-GA4GH standards: - 0 start, half open coordinates - The structuring of POST inputs, redirects and other non-reads data will be protobuf3 compatible JSON

Bioconductor/Rhtsget documentation built on May 7, 2019, 8:40 a.m.