query_vcf: Query VCF file

In RajLabMSSM/echotabix: echoverse module: automated creation and querying of tabix files

Query VCF file

Description

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

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)

RajLabMSSM/echotabix documentation built on Nov. 21, 2023, 8:02 a.m.