Opération de maintenance au data center INRAE de Toulouse du jeudi 20 mars à 15h00 au lundi 24 Mars 2025 à 13h
Les services ForgeMia et Mattermost seront donc inaccessibles pendant cette période (plus de détails)
\texttt{spell-marker} understand a few common formats, based on MapMaker RAW format (without traits) :
\begin{itemize}
\item A line beginning with {\tt data type} followed by ignored text
\item A line containing four integer values : number of markers, number of individuals, two ignored values
\item A line per marker beginning with starred(*) marker name followed by a space and by allele observed or inferred for each individual (a character per individual).
\end{itemize}
Build in allele code are :
\begin{description}
\item[02] SNP observations, where 0 and 2 are homozygous and 1 is heterozygous. These observations type are relevant for any individual in the pedigree.
\item[ABHCD] MapMaker like Parental Origin inferred observations. These are relevant for inbred lines crosses products. Let's consider the cross $A|A \times B|B$:
\begin{itemize}
\item The child is typed A and the allele A is not dominant. The only possible genotype is $A|A$. This is encoded by the character {\tt A} in MapMaker.
\item The child is typed A and the allele A is dominant. The possible genotype are $A|A$, $A|B$ and $B|A$. This is encoded by the character {\tt D} in MapMaker.
\item The child is typed B and the allele B is not dominant. The only possible genotype is $B|B$. This is encoded by the character {\tt B} in MapMaker.
\item The child is typed B and the allele B is dominant. The possible genotype are $A|B$, $B|A$ and $B|B$. This is encoded by the character {\tt C} in MapMaker.
\item The child is typed AB (the allele A and B are codominant). The possible genotype are $A|B$ and $B|A$. This is encoded by the character {\tt H} in MapMaker.
\item The child in not typed. The possible genotypes are $A|A$, $A|B$, $B|A$ and $B|B$. This is encoded by the character {\tt -} in MapMaker.
\end{itemize}
The parental origin letters can be overridden in the command line.
\item[CP] Outbred observations as defined in Cathagene. These observations are relevant for all known phases situations, including cases where one parent is homozygous, when 3 or 4 different alleles are present. Lets consider the cross $A|B \times C|D$: The possibles child genotypes are $A|C$, $A|D$, $B|C$ and $B|D$. Carthagene format actually enables the user to express any subset of the 4 different possibilities using a single hexadecimal digit (0-f).
\begin{center}
\begin{tabular}{cc}
Code & Possible genotypes \\
\hline
1 &$A|C$\\
2 &$A|D$\\
3 &$A|C$,$A|D$\\
4 &$B|C$\\
5 &$A|C$,$B|C$\\
6 &$A|D$,$B|C$\\
7 &$A|C$,$A|D$,$B|C$\\
8 &$B|D$\\
9 &$A|C$,$B|D$\\
a &$A|D$,$B|D$\\
b &$A|C$,$A|D$,$B|D$\\
c &$B|C$,$B|D$\\
d &$A|C$,$B|C$,$B|D$\\
e &$A|D$,$B|C$,$B|D$\\
0 or f or - &$A|C$,$A|D$,$B|C$,$B|D$\\
\end{tabular}
\end{center}
\end{description}
Other allele code can be defined via a JSON file. (see appendix \ref{ch:spell:marker} for format and sample files)
