From ca1c11d43ce7b9871f4c93521f40acaa31e08771 Mon Sep 17 00:00:00 2001
From: Jody Phelan <jody.phelan@lshtm.ac.uk>
Date: Mon, 21 Oct 2024 22:21:13 +0100
Subject: [PATCH] add dp4 support in var into

---
 pathogenprofiler/vcf.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/pathogenprofiler/vcf.py b/pathogenprofiler/vcf.py
index 6050b1d..d8a084b 100644
--- a/pathogenprofiler/vcf.py
+++ b/pathogenprofiler/vcf.py
@@ -23,6 +23,9 @@ def get_stand_support(var: pysam.VariantRecord,alt: str) -> Tuple[int,int]:
     elif 'SB' in var.samples[0]:
         forward_support = var.samples[0]['SB'][(alt_index+1)*2]
         reverse_support = var.samples[0]['SB'][(alt_index+1)*2+1]
+    elif 'DP4' in var.info:
+        forward_support = var.info['DP4'][alt_index*2]
+        reverse_support = var.info['DP4'][alt_index*2+1]
     else:
         forward_support = None
         reverse_support = None