From 1a6fb6b69fe68e9819cda5521f60b126a025bb9b Mon Sep 17 00:00:00 2001
From: Daniel Cameron <daniel.l.cameron@gmail.com>
Date: Tue, 20 Jun 2023 22:48:53 +1000
Subject: [PATCH] Replaced deprecated DPADJ/CNADJ fields in example

---
 VCFv4.4.tex | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)
 mode change 100644 => 100755 VCFv4.4.tex

diff --git a/VCFv4.4.tex b/VCFv4.4.tex
old mode 100644
new mode 100755
index 055d5b9f9..85fcf3ec6
--- a/VCFv4.4.tex
+++ b/VCFv4.4.tex
@@ -1583,10 +1583,10 @@ \subsubsection{Sample mixtures}
 \begin{flushleft}
 \begin{tabular}{ l l l l l l l l l l l }
 \#CHROM & POS & ID & REF & ALT & QUAL & FILTER & INFO & FORMAT & Blood & TissueSample\\
-2 & 321681 & bnd\_W & G & G$]2:421681]$ & 6 & PASS & MATEID=bnd\_U & GT:DPADJ & 0:32 & $0|1:9,21$ \\
-2 & 321682 & bnd\_V & T & $[2:421682[$T & 6 & PASS & MATEID=bnd\_X & GT:DPADJ & 0:29 & $0|1:11,25$ \\
-13 & 421681 & bnd\_U & A & A$]2:321681]$ & 6 & PASS & MATEID=bnd\_W & GT:DPADJ & 0:34 & $0|1:10,23$ \\
-13 & 421682 & bnd\_X & C & $[2:321682[$C & 6 & PASS & MATEID=bnd\_V & GT:DPADJ & 0:31 & $0|1:8,20$ \\
+2 & 321681 & bnd\_W & G & G$]2:421681]$ & 6 & PASS & MATEID=bnd\_U & GT:AD & 0:32,0 & $0|1:9,21$ \\
+2 & 321682 & bnd\_V & T & $[2:421682[$T & 6 & PASS & MATEID=bnd\_X & GT:AD & 0:29,0 & $0|1:11,25$ \\
+13 & 421681 & bnd\_U & A & A$]2:321681]$ & 6 & PASS & MATEID=bnd\_W & GT:AD & 0:34,0 & $0|1:10,23$ \\
+13 & 421682 & bnd\_X & C & $[2:321682[$C & 6 & PASS & MATEID=bnd\_V & GT:AD & 0:31,0 & $0|1:8,20$ \\
 \end{tabular}
 \end{flushleft}
 \normalsize
@@ -1599,10 +1599,10 @@ \subsubsection{Sample mixtures}
 \begin{flushleft}
 \begin{tabular}{ l l l l l l l l l l l }
 \#CHROM & POS & ID & REF & ALT & QUAL & FILTER & INFO & FORMAT & Blood & TumorSample \\
-2 & 321681 & bnd\_W & G & G$]2:421681]$ & 6 & PASS & MATEID=bnd\_U & GT:CNADJ & 0:1 & 1:1 \\
-2 & 321682 & bnd\_V & T & $[2:421682[$T & 6 & PASS & MATEID=bnd\_X & GT:CNADJ & 0:1 & 1:1 \\
-13 & 421681 & bnd\_U & A & A$]2:321681]$ & 6 & PASS & MATEID=bnd\_W & GT:CNADJ & 0:1 & 1:1 \\
-13 & 421682 & bnd\_X & C & $[2:321682[$C & 6 & PASS & MATEID=bnd\_V & GT:CNADJ & 0:1 & 1:1 \\
+2 & 321681 & bnd\_W & G & G$]2:421681]$ & 6 & PASS & MATEID=bnd\_U & GT:CN & 0:1 & 1:1 \\
+2 & 321682 & bnd\_V & T & $[2:421682[$T & 6 & PASS & MATEID=bnd\_X & GT:CN & 0:1 & 1:1 \\
+13 & 421681 & bnd\_U & A & A$]2:321681]$ & 6 & PASS & MATEID=bnd\_W & GT:CN & 0:1 & 1:1 \\
+13 & 421682 & bnd\_X & C & $[2:321682[$C & 6 & PASS & MATEID=bnd\_V & GT:CN & 0:1 & 1:1 \\
 \end{tabular}
 \end{flushleft}
 \normalsize