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Cristina Yenyxe Gonzalez Garcia
authoredJul 24, 2019
Restructured where is PEDIGREE meta explained
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‎VCFv4.3.tex

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@@ -248,12 +248,23 @@ \subsubsection{Pedigree field format}
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##PEDIGREE=<ID=ChildID,Father=FatherID,Mother=MotherID>
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##PEDIGREE=<ID=SampleID,Name_1=Ancestor_1,...,Name_N=Ancestor_N>
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\end{verbatim}
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\noindent or a link to a database:
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The first two lines assert that the DNA in genomes TumourSample and SomaticNonTumour is asexually or clonally derived with mutations from the DNA in genome OriginalID.
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The third line describes a family relationship between genomes.
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A VCF will therefore contain one entry per trio.
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The fourth line is an example of the most general form of a pedigree line.
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It means that the genome SampleID is derived from the N $\ge$ 1 genomes Ancestor1, ..., AncestorN.
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TODO: Text describing meaning of Mother and Father well-known ancestor tags
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and explaining how to represent a PED file as in-line \#\#PEDIGREE trios.
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Noting alternatively to use \#\#pedigreeDB=URL to point to an external PED file.
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\noindent If samples and the relationships between them are described in an external resource such as a database or PED file, is it also possible to provide a link:
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\begin{verbatim}
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##pedigreeDB=URL
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\end{verbatim}
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\noindent See \ref{ClonalPedigree} (clonal relationships) and \ref{FamilialPedigree} (trios and families) for details.
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\noindent See \ref{ClonalPedigree} for more details about clonal relationships.
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\subsection{Header line syntax}
@@ -1258,11 +1269,6 @@ \subsubsection{Clonal derivation relationships}
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\end{verbatim}
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This line asserts that the DNA in genome DerivedID is asexually or clonally derived with mutations from the DNA in genome OriginalID.
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This is the asexual analog of the VCF format that has been proposed for family relationships between genomes (see~\ref{FamilialPedigree}), in which there is one entry per trio of the form:
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\begin{verbatim}
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##PEDIGREE=<ID=ChildID,Mother=MotherID,Father=FatherID>
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\end{verbatim}
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Let's consider a cancer patient VCF file with 4 genomes: germline, primary\_tumor, secondary\_tumor1, and secondary\_tumor2 as illustrated in Figure 10.
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The primary\_tumor is derived from the germline and the secondary tumors are each derived independently from the primary tumor, in all cases by clonal derivation with mutations.
@@ -1380,19 +1386,6 @@ \subsection{Representing unspecified alleles and REF-only blocks (gVCF)}
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\end{flushleft}
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\normalsize
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\subsection{Describing family relationships}
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\label{FamilialPedigree}
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This is the VCF format that has been proposed for family relationships between genomes, in which there is one entry per trio of the form:
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\begin{verbatim}
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##PEDIGREE=<ID=ChildID,Mother=MotherID,Father=FatherID>
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\end{verbatim}
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TODO: Text describing meaning of Mother and Father well-known ancestor tags
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and explaining how to represent a PED file as in-line \#\#PEDIGREE trios.
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Noting alternatively to use \#\#pedigreeDB=URL to point to an external PED file.
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\pagebreak
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\section{BCF specification}
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