From 09a9c442d0e3e2ebe12cef6bf85ed2aa322c878f Mon Sep 17 00:00:00 2001 From: John Marshall Date: Mon, 19 Aug 2019 15:57:50 +0100 Subject: [PATCH] Apply @lbergelson's wording tweak; add "1-based" --- VCFv4.3.tex | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/VCFv4.3.tex b/VCFv4.3.tex index cc4ffbb73..2e7e3c2f7 100644 --- a/VCFv4.3.tex +++ b/VCFv4.3.tex @@ -372,8 +372,8 @@ \subsubsection{Fixed fields} \begin{itemize} \renewcommand{\labelitemii}{$\circ$} -\item END: End reference position, indicating that the variant spans positions POS--END on reference/contig CHROM. -Normally this is the position of the last base in the REF allele, so can be derived from POS and the length of REF, and no END INFO field is needed. +\item END: End reference position (1-based), indicating the variant spans positions POS--END on reference/contig CHROM. +Normally this is the position of the last base in the REF allele, so it can be derived from POS and the length of REF, and no END INFO field is needed. However when symbolic alleles are used, e.g.\ in gVCF or structural variants, an explicit END INFO field provides variant span information that is otherwise unknown. This field is used to compute BCF's {\tt rlen} field (see~\ref{BcfSiteEncoding}) and is important when indexing VCF/BCF files to enable random access and querying by position.