From 5832b924543482ebce00e3e3b0625a89c287eb71 Mon Sep 17 00:00:00 2001
From: boasvdp <boasvdp@gmail.com>
Date: Tue, 6 Feb 2024 16:13:32 +0100
Subject: [PATCH] feat: include unfiltered variants in tsv output

---
 workflow/rules/mtb_typing.smk | 1 +
 1 file changed, 1 insertion(+)

diff --git a/workflow/rules/mtb_typing.smk b/workflow/rules/mtb_typing.smk
index 3f62af8..04f1ef8 100644
--- a/workflow/rules/mtb_typing.smk
+++ b/workflow/rules/mtb_typing.smk
@@ -170,6 +170,7 @@ rule mtb_annotated_vcf_to_table:
 FIELDS=$(python workflow/scripts/print_fields_VariantsToTable.py {params.metadata:q},{params.effect_column:q})
 gatk VariantsToTable \
 -V {input.vcf} \
+--show-filtered \
 -F CHROM \
 -F POS \
 -F TYPE \