Phylogenetic-Tree Pipeline

An emsembled software easy for inferring clones from mutations.

Dependencies

PhyloWGS:python2, NumPy and SciPy (python2), ETE2 (python2), GSL SciClone:R (version >= 3.5), IRanges, devtools, Pyclone: python (version>2), numpy, pandas

Guide

Command for PhylowGS

ct/CRI/Zhu_lab/s171162/Tree/data/input_files/TCGA_SKCM/TCGA-D9-A148-06.maf.txt -cnv_file /project/CRI/Zhu_lab/s171162/Tree/data/inpu\
t_files/TCGA_SKCM/TCGA-D9-A148-06.cnv.txt  -output_dir /project/CRI/Zhu_lab/s171162/Tree/phylogenic_tree/test_output6 -phylo_code /p\
roject/CRI/Zhu_lab/s171162/Tree/package/phylowgs-master/

Command for PyClone

t/CRI/Zhu_lab/s171162/Tree/data/input_files/TCGA_SKCM/TCGA-D9-A148-06.maf.txt -cnv_file /project/CRI/Zhu_lab/s171162/Tree/data/input\
_files/TCGA_SKCM/TCGA-D9-A148-06.cnv.txt  -output_dir /project/CRI/Zhu_lab/s171162/Tree/phylogenic_tree/test_output6 -phylo_code /pr\
oject/CRI/Zhu_lab/s171162/Tree/package/phylowgs-master/

Command for SciClone

ct/CRI/Zhu_lab/s171162/Tree/data/input_files/TCGA_SKCM/TCGA-D9-A148-06.maf.txt -cnv_file /project/CRI/Zhu_lab/s171162/Tree/data/inpu\
t_files/TCGA_SKCM/TCGA-D9-A148-06.cnv.txt  -output_dir /project/CRI/Zhu_lab/s171162/Tree/phylogenic_tree/test_output6 -phylo_code /p\
roject/CRI/Zhu_lab/s171162/Tree/package/phylowgs-master/