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tCoNuT Workflow

Example plots

Plotting of copy number

Rscript --vanilla ${tCoNuTdir}/plotting/plotCGH_EXOME.R ${OFILE}.cna.tsv ${OFILE}.amp.tsv ${OFILE}.del.tsv ${OFILE}

Plotting of copy number with hets superimposed

Rscript --vanilla ${tCoNuTdir}/plotting/plotCGHwithHets.R ${OFILE}.cna.tsv ${OFILE}.amp.tsv ${OFILE}.del.tsv ${OFILE}.hets.tsv ${OFILE}_withhets

Plotting of BAF

Rscript --vanilla ${tCoNuTdir}/plotting/plotBAF.R baf.txt ${OFILE}.baf

Linear Genome Plotting of CNA and BAF (both scripts are MATLAB code)

MCRPATH=/packages/MCR/9.0/v90
${tCoNuTdir}/plotting/plotLinearCNA/run_plotLinearCNAandBAF.sh ${MCRPATH} ${OFILE}.cna.tsv baf.txt ${OFILE}.cnaBAF.png

${tCoNuTdir}/plotting/plotLinearCNAabsBAF/run_plotLinearCNAandAbsBAF.sh ${MCRPATH} ${OFILE}.cna.tsv baf.txt ${OFILE}.cnaAbsBAF.png