Count properly SNPs and INDELS

PathoGenOmics-Lab · Sep 27, 2023 · 8e3c1aa · 8e3c1aa
1 parent 5020acb
commit 8e3c1aa
Showing 1 changed file with 6 additions and 1 deletion.
diff --git a/workflow/scripts/report/NV_description.R b/workflow/scripts/report/NV_description.R
@@ -460,7 +460,12 @@ vcf_snp %>%
 
 # STATS FOR REPORTING
 
-n_indels <- filter(vcf, NV_class == "INDEL") %>% length()
+n_indels <- vcf %>%
+  filter(NV_class == "INDEL") %>%
+  pull(SNP) %>%
+  unique() %>%
+  length()
+
 n_snv <- length(unique(vcf$SNP)) - n_indels
 
 list(