From 281175b77992238cd1f2644d507368b898355039 Mon Sep 17 00:00:00 2001
From: Jacob Morrison <Jacob.Morrison@vai.org>
Date: Tue, 29 Oct 2024 14:36:39 -0400
Subject: [PATCH] add note about min covg in vcf2bed

---
 docs/methylextraction.md | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/docs/methylextraction.md b/docs/methylextraction.md
index 3c2adc9..dd96c77 100644
--- a/docs/methylextraction.md
+++ b/docs/methylextraction.md
@@ -13,6 +13,9 @@ file:
 ```bash
 $ biscuit vcf2bed -t cg my_pileup.vcf.gz > my_pileup.bed
 ```
+For BISCUIT version 1.5.0 and earlier, the minimum coverage by default is 3. This setting was good for traditional WGBS;
+however, for low input and single cell protocols, this option should be changed to 1 (`biscuit vcf2bed -k 1 ...`).
+BISCUIT version 1.6.0 and later have the default value switched to 1 to avoid user confusion.
 
 The `-t` flag can be used to retrieve mutation and other information, including