feat: include unfiltered variants in tsv output

RIVM-bioinformatics · Feb 6, 2024 · 5832b92 · 5832b92
1 parent 794a7a9
commit 5832b92
Showing 1 changed file with 1 addition and 0 deletions.
diff --git 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 \