convert: Convert to tabix

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

Convert to tabix

Description

Convert a tabular file to compressed (bgzip), indexed, tabix format for rapid querying.

Usage

convert(
  target_path,
  bgz_file = construct_tabix_path(target_path = target_path),
  chrom_col = "CHR",
  start_col = "POS",
  end_col = start_col,
  comment_char = NULL,
  format = NULL,
  convert_methods = list(sort_coordinates = "bash", run_bgzip = "Rsamtools", index =
    "Rsamtools"),
  conda_env = "echoR_mini",
  force_new = TRUE,
  verbose = TRUE
)

Arguments

target_path	Path to full GWAS/QTL summary statistics file.
bgz_file	Path to resulting bgz-compressed file after target_path has been converted to tabix format.
chrom_col	Name of the chromosome column in the target_path file.
start_col	Name of the genomic start position column in the target_path file.
end_col	Name of the genomic end position column in the target_path file.
comment_char	A single character which, when present as the first character in a line, indicates that the line is to be omitted from indexing.
format	Format of the target_path file: "vcf" or "table".
convert_methods	A named list containing methods to run each step with.
conda_env	Conda environments to search in. If NULL (default), will search all conda environments.
force_new	Force the creation of a new bgzip file (.bgz) and a new tabix index file (.tbi).
verbose	Print messages.

Source

samtools/tabix GitHub repo

Rhtslib (which Rsamtools and seqminer depend on for tabix) is very out of date (1.7 vs. 1.15).

conda install tabix was recently fixed so it installs htslib

See Also

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

Examples

#### Example with full data ####
# tmp <- echodata::example_fullSS()
#### Example with single locus ####
dat <- echodata::BST1
tmp <- tempfile()
data.table::fwrite(dat, tmp, sep="\t")
 
tabix_files <- echotabix::convert(target_path = tmp)

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