diff --git a/workflow/scripts/format_vcf_fields_longer.R b/workflow/scripts/format_vcf_fields_longer.R index 26c5512..a1584f3 100644 --- a/workflow/scripts/format_vcf_fields_longer.R +++ b/workflow/scripts/format_vcf_fields_longer.R @@ -27,13 +27,19 @@ filter.exclude <- lapply(snakemake@params$filter_exclude, empty.to.na) # Process input table log_info("Applying filters and writing results") -read_tsv(snakemake@input$tsv) %>% +read_tsv( + snakemake@input$tsv, + col_types = cols( + POS = col_integer(), + .default = col_character() + ) +) %>% # Separate -delimited "...[*]..." columns (e.g. ANN[*].EFFECT) separate_rows( contains("[*]"), sep = snakemake@params$sep, - convert = TRUE + convert = FALSE ) %>% # Rename "...[*]..." columns using the provided lookup via Snakemake config