diff --git a/VCFv4.4.tex b/VCFv4.4.tex old mode 100644 new mode 100755 index 055d5b9f9..5e62456bd --- 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 @@ -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.