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Query VCF file

Source: R/query_vcf.R
query_vcf.Rd

Query a Variant Call Format (VCF) file. The VCF file can be either local or remote.

Usage

query_vcf(
  target_path,
  target_index = paste0(target_path, ".tbi"),
  target_genome = "GRCh37",
  query_granges,
  samples = character(),
  method = c("variantannotation", "conda", "rtracklayer", "seqminer"),
  overlapping_only = FALSE,
  query_save = TRUE,
  save_path = construct_vcf_path(target_path = target_path, query_granges =
    query_granges),
  force_new = FALSE,
  as_datatable = FALSE,
  cleanup_tbi = TRUE,
  conda_env = "echoR_mini",
  verbose = TRUE
)

Arguments

target_path

Path to local VCF file or remote URL.

target_index

Tabix index file for target_path.

target_genome

Genome build of the VCF file.

query_granges

GRanges object to be used for querying the target_path file. Alternatively, can be variant-level summary statistics to be converted into a GRanges object by construct_query.

samples

[Optional] Sample names to subset the VCF by. If this option is used, the GRanges object will be converted to a ScanVcfParam for usage by readVcf.

method

Method to query VCF with.

overlapping_only

Remove variants that do not overlap with the positions in query_dat.

query_save

Whether to save the results of the query on disk. Note: Writing to disk can take some time.

save_path

File path to save query subset to (as VCF).

force_new

Force the creation of a new VCF subset file even if one exists.

as_datatable

Return the VCF subset file as a data.table (using vcf_to_dt). If save_path=TRUE the file will still be saved as a bgzip-compressed VCF file.

cleanup_tbi

Remove local copies of tabix index file (.tbi) after completing queries.

conda_env

Conda environments to search in. If NULL (default), will search all conda environments.

verbose

Print messages.

Value

VCF object, or data.table (when as_datatable=TRUE).

See also

Other tabix functions: construct_tabix_path(), construct_vcf_path(), convert(), index, query_table(), read_bgz(), run_bgzip()

Examples

if (FALSE) { # \dontrun{
query_dat <- echodata::BST1
target_path <- system.file("extdata", "BST1.1KGphase3.vcf.bgz",
                    package = "echodata")

#### Import ####
vcf <-  query_vcf(
    query_granges = query_dat,
    target_path = target_path)
} # }