From 6c1092ff23e48039916bc5e245bc89ae56eac466 Mon Sep 17 00:00:00 2001
From: Wytamma Wirth <wytamma.wirth@me.com>
Date: Fri, 19 Jul 2024 11:34:10 +1000
Subject: [PATCH] Add core.txt format

---
 README.md | 13 +++++++++++++
 1 file changed, 13 insertions(+)

diff --git a/README.md b/README.md
index 4ebde8b..732a3f2 100644
--- a/README.md
+++ b/README.md
@@ -143,6 +143,19 @@ GENE | The `/gene` tag of the feature (if it existed)
 PRODUCT | The `/product` tag of the feature (if it existed)
 EFFECT | The `snpEff` annotated consequence of this variant (ANN tag in .vcf)
 
+## Columns in TXT format
+
+Name | Description
+-----|------------
+ID | Reference + Sample
+LENGTH | Length of the reference
+ALIGNED | Number of sites aligned to
+UNALIGNED | Number of sites unaligned
+VARIANT | Number of sites different from the reference
+HET | Number of sites heterozygous or poor quality genotype represented with an n (`--minqual`)
+MASKED | Number of sites masked in reference represented with an X (`--mask`)
+LOWCOV | Number of sites low coverage in this sample represented with an N (`--mincov`)
+
 ## Variant Types
 
 Type | Name | Example