docs

Author: Li Tai Fang

docs/Manual.pdf

@@ -140,8 +140,6 @@ \subsection{To train data set into a classifier}
 --inclusion-region  validated.bed
 --truth-snv         truth.snp.vcf \
 --truth-indel       truth.indel.vcf \
---pass-threshold    0.5 \
---lowqual-threshold 0.1 \
 --output-dir        $OUTPUT_DIR
 \end{lstlisting}
 
@@ -182,6 +180,8 @@ \subsection{To predict somatic mutation based on trained classifiers}
 --inclusion-region validated.bed
 --classifier-snv   sSNV.Classifier.RData \
 --classifier-indel sINDEL.Classifier.RData \
+--pass-threshold    0.5 \
+--lowqual-threshold 0.1 \
 --output-dir       $OUTPUT_DIR
 
 \end{lstlisting}
@@ -589,6 +589,9 @@ \section{Future development}
   \item
   Develop a version for deep sequencing cfDNA/ctDNA.
 
+  \item
+  Dockerize SomaticSeq
+  
 \end{itemize}