README.md

In seandavi/VCFWrenchR: VCF file utilities

Installation

devtools::install_github('seandavi/VCFWrenchR')

Very basic usage

Read in a VCF file using VariantAnnotation.

library(VariantAnnotation)
vcffile = system.file(package='VariantAnnotation',path='extdata/chr22.vcf.gz')
v = readVcf(vcffile,'hg19')
head(v)
````

## Convert to data.frame

```{r}
head(as.data.frame(v))

Convert to JSON

as.json(head(v,2),pretty=TRUE)

Write line-delimited json

con = tempfile()
jsonlite::stream_out(as.data.frame(v),con)
close(con)

Working with jq and ElasticSearch

Load line-delimited json variants into ElasticSearch

TODO: Do this in R....

# assumes jq installed
cat abc.json | \
    jq -c '. | {"index": {"_index": "variants", "_type": "variant"}}, .' | \
    curl -XPOST localhost:9200/_bulk --data-binary @-

seandavi/VCFWrenchR documentation built on May 29, 2019, 4:53 p.m.