Rebased #434 onto VCFv4.5

VCFv4.5.draft.tex

@@ -17,7 +17,7 @@
 \renewcommand{\thefootnote}{\fnsymbol{footnote}}
 
 \begin{document}
-\input{VCFv4.5.ver}
+\input{VCFv4.5.draft.ver}
 \title{\huge \color{red} DRAFT SPEC SUBJECT TO CHANGE \\ The Variant Call Format Specification \\ \vspace{0.5em} \large VCFv4.5 and BCFv2.2}
 \date{\headdate}
 \maketitle
@@ -482,6 +482,10 @@ \subsubsection{Genotype fields}
       GQ		& 1		& Integer	& Conditional genotype quality \\
       GT		& 1		& String	& Genotype \\
       HQ		& 2		& Integer	& Haplotype quality \\
+      LAA		& .		& Integer	& Strictly increasing, 1-based indices into ALT, indicating which alternate alleles are relevant (local) for the current sample \\
+      LAD		& .		& Integer	& Read depth for the reference and each of the local alternate alleles listed in LAA \\
+      LGT		& .		& String 	& Genotype against the local alleles \\
+      LPL		& .		& Integer	& Phred-scaled genotype likelihoods rounded to the closest integer for genotypes that involve the reference and the local alternative alleles listed in LAA \\
       MQ		& 1		& Integer	& RMS mapping quality \\
       PL		& G		& Integer	& Phred-scaled genotype likelihoods rounded to the closest integer \\
       PP		& G		& Integer	& Phred-scaled genotype posterior probabilities rounded to the closest integer \\
@@ -578,6 +582,38 @@ \subsubsection{Genotype fields}
     \end{itemize}
 
   \item HQ (Integer): Haplotype qualities, two comma separated phred qualities.
+  \item LAA is a sorted list of $n$ distinct integers, where $1 \le n \le \left|\mathrm{ALT}\right|$, giving the (1-based) indices within ALT of the alleles that are observed in the sample.
+  In callsets with many samples, sites may grow to include numerous alternate alleles at the same POS.
+  Usually, few of these alleles are actually observed in any one sample, but each genotype must supply fields like PL and AD for all of the alleles---a very inefficient representation as PL's size is quadratic in the allele count.
+  Similarly, in rare sites, which can be the bulk of the sites, the vast majority of the samples are reference.
+  To prevent this growth in VCF size, one can choose to specify the genotype, allele depth and the genotype likelihood against a subset of ``Local Alleles''.
+  LAA is the strictly increasing, 1-based index into ALT, pointing out the alternative alleles that are actually in-play for that sample.
+  LAD is the depth of the local alleles,
+  LPL is subset of the PL array that pertains to the alleles that are REF or referred to by LAA,
+  LGT is the genotype but referencing the local alleles rather than the global ones.
+  It is implicit that REF is part of any ``local'' context, and it always has index 0, even if the genotype is compound HET.
+  For example, if REF is G, ALT is A,C,T,\verb!<*>! and a genotype only has information about G, C, and \verb!<*>!, one can have LAA=[2,4] and thus LPL will be interpreted as pertaining to the alleles [G, C, \verb!<*>!] and not contain likelihood values for genotypes that involve A or T.
+  In this case LGT=0/1 means that the sample is G/C.
+  GQ is still the genotype quality, even when the genotype is given against the local alleles.
+  Note that reordering might be required and care need to be taken to reorder LAD and LPL appropriately.
+  LAA is required in order to interpret LAD, LPL, and LGT.
+  In the following example, the records with the same POS encode the same information (some columns removed for clarity):
+  \begin{tabular}[l]{llllll}
+  	POS &REF&  ALT&FORMAT&sample\\
+  	1&G&A,C,T,\textless*\textgreater& LAA:LGT:LAD:LPL&  2,4:1/1:20,30,10:90,80,0,100,110,120\\
+  	1&G&A,C,T,\textless*\textgreater& GT:AD:PL&  2/2:20,.,30,.,10:90,.,.,80,.,0,.,.,.,.,100,.,110,.,120\\
+  	2&A&C,G,T,\textless*\textgreater& LAA:LGT:LAD:LPL& 3:0/1:15,25:40,0,80\\
+  	2&A&C,G,T,\textless*\textgreater& GT:AD:PL&0/3:15,.,.,25,.:40,.,.,.,.,.,0,.,.,80,.,.,.,.\\
+  	3&C&G,T,\textless*\textgreater& LAA:LGT:LAD:LPL& 4:0/0:30,1:0,30,80\\
+  	3&C&G,T,\textless*\textgreater& GT:AD:PL& 0/0:30,.,.1:0,.,.,.,.,.,.,.,.,.,30,.,.,.,80\\
+  	4&G&A,T,\textless*\textgreater& LAA:LGT:LAD:LPL& :0/0:30:0\\
+  	4&G&A,T,\textless*\textgreater& GT:AD:PL& 0/0:30,.,..:0,.,.,.,.,.,.,.,.,.,.,.,.,.,.\\
+  \end{tabular}
+  \item LAD: is a list of $n+1$ integers giving read depths (as per AD) for the REF allele and each of the local alleles as listed in LAA.
+  \item LGT: is the genotype, encoded as allele indexes separated by either of $/$ or $\mid$, as with GT, however, the indexes are into the list consisting of REF and the ALTs referenced by LAA.
+  So that in the case that LAA is 2,3, LGT=0/2 is equivalent to GT=0/3 and LGT=1/2 is equivalent to GT=2/3 (see example above).
+  \item LPL: is a list of $n+1 \choose \mathrm{Ploidy}$ integers giving phred-scaled genotype likelihoods (rounded to the closest integer; as per PL) for all possible genotypes given the set of alleles defined in the REF and LAA local alleles.
+  The precise ordering is defined in the GL paragraph.
   \item MQ (Integer): RMS mapping quality, similar to the version in the INFO field.
   \item PL (Integer): The phred-scaled genotype likelihoods rounded to the closest integer, and otherwise defined in the same way as the GL field.
   \item PP (Integer): The phred-scaled genotype posterior probabilities rounded to the closest integer, and otherwise defined in the same way as the GP field.
@@ -2552,6 +2588,7 @@ \section{List of changes}
 \subsection{Changes between VCFv4.5 and VCFv4.4}
 
 \begin{itemize}
+	\item Added local allele support
 \end{itemize}
 
 \subsection{Changes between VCFv4.4 and VCFv4.3}