query_vcf_conda: Query VCF: 'conda'

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

Query VCF: conda

Description

Query a subset of a VCF file (remote or local) using tabix via echoconda. Advantages:

• Fast.

• Not dependent on any R packages.

Usage

query_vcf_conda(
  target_path,
  query_granges,
  samples = character(),
  download_index = FALSE,
  query_save = FALSE,
  save_path = NULL,
  conda_env = "echoR_mini",
  verbose = TRUE
)

Arguments

target_path	Path to local VCF file or remote URL.
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.
download_index	Whether to download the index when querying. Corresponds to the -D argument in tabix.
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).
conda_env	Conda environments to search in. If NULL (default), will search all conda environments.
verbose	Print messages.

Value

CollapsedVCF object.

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