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Sample ID and filter update #414

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Sample ID and filter update #414

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958f373
draft of sample ID and filter update
May 30, 2019
ae2612a
fixing build error
Jul 24, 2019
6369341
oops
Jul 24, 2019
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Jul 24, 2019
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5 changes: 4 additions & 1 deletion VCFv4.2.tex
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Original file line number Diff line number Diff line change
Expand Up @@ -141,9 +141,12 @@ \subsubsection{Sample field format}
It is possible to define sample to genome mappings as shown below:
\small
\begin{verbatim}
##SAMPLE=<ID=S_ID,Genomes=G1_ID;G2_ID; ...;GK_ID,Mixture=N1;N2; ...;NK,Description=S1;S2; ...;SK>
##SAMPLE=<ID=S_ID,FILTER=PASS,Genomes=G1_ID;G2_ID; ...;GK_ID,Mixture=N1;N2; ...;NK,Description=S1;S2; ...;SK>
\end{verbatim}
\normalsize
ID is a string that identifies the sample. It comprises of non-whitespace characters and doesn't include the comma (`,') character.
FILTER is a string that has been defined in a \verb!##FILTER! line, except for PASS or `.' which mean that the sample passes or that the filter is missing (respectively).

\subsubsection{Pedigree field format}
It is possible to record relationships between genomes using the following syntax:
\begin{verbatim}
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7 changes: 7 additions & 0 deletions VCFv4.3.tex
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Expand Up @@ -240,6 +240,13 @@ \subsubsection{Sample field format}
##SAMPLE=<ID=Sample2,Assay=Exome,Ethnicity=CEU,Disease=Cancer,Tissue=Breast,Description="European patient exome from breast cancer">
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need to add FILTER to the line itself.

\end{verbatim}}

In the \verb!SAMPLE! line:
\begin{itemize}
\item{ID} is a string that identifies the sample.
It comprises non-whitespace characters and doesn't include the comma (`.') character.
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Comma in the parentheses 😄

\item{FILTER} is a string that has been defined in a \verb!##FILTER! line, except for PASS or `.' which mean that the sample passes or that the filter is missing (respectively).
\end{itemize}

\subsubsection{Pedigree field format}
It is possible to record relationships between genomes using the following syntax:
\begin{verbatim}
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