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Fix typos (VCF) #699

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Fix typos (VCF) #699

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8 changes: 4 additions & 4 deletions VCFv4.4.tex
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Expand Up @@ -607,12 +607,12 @@ \subsubsection{Genotype fields}
\end{tabular}

\item PSO (List of integers): List of phase set ordinals.
For each phase-set name, defines the order in which variants are encountered when traversing a derivate chromosome.
For each phase-set name, defines the order in which variants are encountered when traversing a derivative chromosome.
The missing value '$.$' should be used when the corresponding PSO value is missing.
For each phase-set name, PSO should be defined if any allele with that phase-set name on any record is symbolic structural variant or in breakpoint notation.
Variants in breakpoint notation must have the same PSL and PSO on both records.

Without explicitly specifying the derivate chromosome traversal order, multiple derivate chromosome reconstructions are possible.
Without explicitly specifying the derivative chromosome traversal order, multiple derivative chromosome reconstructions are possible.
Take for example this tandem duplication in a triploid organism with SNVs (ID/QUAL/FILTER columns removed for clarity):

\vspace{0.5em}
Expand Down Expand Up @@ -829,7 +829,7 @@ \section{INFO keys used for structural variants}
\item BFB - breakage fusion bridge
\item DOUBLEMINUTE - Double minute
\end{itemize}
The sematics of other $EVENTTYPE$ values is implementation-defined.
The semantics of other $EVENTTYPE$ values is implementation-defined.
The use of $EVENT$ is not restricted to structural variation and can also be used to associate non-symbolic alleles.
Such linking is useful for scenarios such as kataegis or when there is variant position ambiguity in segmentally duplicated regions.

Expand Down Expand Up @@ -2555,7 +2555,7 @@ \subsection{Changes between VCFv4.4 and VCFv4.3}
\item Added tandem repeat support ($<$CNV:TR$>$, RN, RUS, RUL, RB, CIRB, RUC, CIRUC, RUB)
\item Redefined INFO CN as allele-specific copy number and FORMAT CN as total copy number.
\item Redefined INFO and FORMAT CN to support non-integer copy numbers.
\item Added support for phasing and derivate chromosome reconstruction in the presence of SVs (PSL, PSO, PSQ)
\item Added support for phasing and derivative chromosome reconstruction in the presence of SVs (PSL, PSO, PSQ)
\item Added SVCLAIM to disambiguate copy number based $<$DEL$>$ and $<$DUP$>$ variants from breakpoint based ones.
\item Conceptually separated variant detection and interpretation.
\item Added EVENTTYPE/EVENT to enable the multiple records encoding complex genomic rearrangements to be grouped together.
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