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Resolve #707: remove remaining *ADJ references #729

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merged 2 commits into from
Aug 22, 2023
Merged

Resolve #707: remove remaining *ADJ references #729

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1a6fb6b
Replaced deprecated DPADJ/CNADJ fields in example
d-cameron Jun 20, 2023
d1e01e4
#707 Clarified in change log that DPADJ, CNADJ and CICNADJ have been …
d-cameron Jun 20, 2023
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19 changes: 10 additions & 9 deletions VCFv4.4.tex
100644 → 100755
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand All @@ -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
Expand Down Expand Up @@ -2568,7 +2568,8 @@ \subsection{Changes between VCFv4.4 and VCFv4.3}
\item Clarified CIPOS should be used to define micro-homology bounds
\item Clarified INFO lines field ordering
\item Clarified that symbolic and breakpoint notation ALT alleles are case sensitive.
\item Deprecated SVTYPE, DPADJ, CNADJ, CICNADJ
\item Deprecated SVTYPE
\item Removed DPADJ, CNADJ, CICNADJ
\item Disallowed BND ALT records (these should use breakpoint notation anyway)
\item Removed definition of DP from Section 3 as it was already defined in Section 1.6.1.8.
\item Deprecated bundles in favour of PSL-based phasing.
Expand Down