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Comments (1)

mcanouil avatar mcanouil commented on June 12, 2024

This is normal, "vep_file" is internal when defined eggla_lapply.
Although I simplified this and anyway renamed the main argument to be more consistent with syntax of other arguments.

I believe the issue you are having is somewhere else, i.e.,

eggla/R/run_eggla_gwas.R

Lines 449 to 480 in 1eb2dd5

vcf_file <- sprintf("%s__%s", basename_file, basename(vcf))
results_file <- sub("\\.vcf.gz", "", vcf_file)
cmd <- paste(
bin_path[["bcftools"]],
"+fill-tags", vcf,
"|",
bin_path[["bcftools"]],
"view",
bcftools_view_options,
"--force-samples",
"--samples-file", sprintf("%s.samples", basename_file)
)
if (!is.null(vep_file) && file.exists(vep_file)) {
cmd <- paste(
cmd,
"|",
bin_path[["bcftools"]],
"annotate",
"--annotations", vep_file,
"--header-lines", sub("_formatted.tsv.gz", ".header", vep_file),
"--columns CHROM,POS,Gene,Symbol,rsid",
"|",
bin_path[["bcftools"]],
"annotate",
"--set-id '%INFO/rsid'",
"|",
bin_path[["bcftools"]],
"annotate",
"--set-id +'%CHROM:%POS:%REF:%ALT'",
"--output-type z --output", vcf_file
)

Note that the changes are in the current PR #97

from eggla.

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