query_vcf_rtracklayer: Query VCF: 'rtracklayer'

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

Query VCF: rtracklayer

Description

Query a subset of a VCF file (remote or local) using rtracklayer::import, which is essentially just a wrapper for scanTabix. Advantages of rtracklayer:

• None to speak of.

Disadvantages of rtracklayer:

• Unable to query a subset of samples, unlike scanVcf.

• Unable to return results as a structured CollapsedVCF object.

Usage

query_vcf_rtracklayer(
  target_path,
  target_index = paste0(target_path, ".tbi"),
  query_granges,
  samples = character(),
  query_save = FALSE,
  save_path = NULL,
  verbose = TRUE
)

Arguments

target_path	Path to local VCF file or remote URL.
target_index	Tabix index file for target_path.
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.
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).
verbose	Print messages.

Value

Raw text?

Source

Inconsistencies with rtracklayer

BST1 <- echodata::BST1 query_dat <- BST1[seq(1, 50), ] target_path <- paste( "ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/release/20110521/", "ALL.chr4.phase1_release_v3.20101123.snps_indels_svs.genotypes.vcf.gz", sep="/" ) vcf <- echotabix:::query_vcf_rtracklayer( target_path = target_path, query_granges = query_dat)

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