Obtain the extracted VCF fields in longer format

Author: ahmig

workflow/rules/vaf.smk

@@ -187,6 +187,18 @@ rule extract_vcf_fields:
         'SnpSift extractFields -s {params.sep:q} {input.vcf:q} {params.extract_columns} >{output.tsv:q} 2>{log:q}'
 
 
+rule format_vcf_fields_longer:
+    conda: "../envs/renv.yaml"
+    params:
+        sep = ","
+    input:
+        tsv = OUTDIR/f"{OUTPUT_NAME}.vcf_fields.tsv"
+    output:
+        tsv = OUTDIR/f"{OUTPUT_NAME}.vcf_fields.longer.tsv"
+    script:
+        "../scripts/format_vcf_fields_longer.R"
+
+
 rule vcf_to_tsv:
     threads: 1
     conda: "../envs/renv.yaml"

workflow/scripts/format_vcf_fields_longer.R

@@ -0,0 +1,12 @@
+#!/usr/bin/env Rscript
+
+# Write stdout and stderr to log file
+log <- file(snakemake@log[[1]], open = "wt")
+sink(log, type = "message")
+sink(log, type = "output")
+
+library(tidyverse)
+
+read_tsv(snakemake@input$tsv) %>%
+    separate_rows(contains("[*]"), sep = snakemake@params$sep) %>%
+    write_tsv(snakemake@output$tsv)