Skip to content

Latest commit

 

History

History
116 lines (96 loc) · 4 KB

README.md

File metadata and controls

116 lines (96 loc) · 4 KB

Pysubsim-tree

Introduction

Next-generation sequencing (NGS) and the third generation sequencing (TGS) have recently allowed us to develop algorithms to quantitatively dissect the extent of het- erogeneity within a tumour, resolve cancer evolution history and identify the somatic variations and aneuploidy events. Simulation of tumor NGS and TGS data serves as a powerful and cost-effective approach for benchmarking these algorithms, however, there is no available tool that could simulate all the distinct subclonal genomes with diverse aneuploidy events and somatic variations according to the given tumor evolution history. We provide a simulation package, Pysubsim-tree, which could simulate the tumor genomes according to their evolution history defined by the somatic variations and aneuploidy events.

Pysubsim-tree could be run individually or strung with art_illumina, bwa and samtools to generate Next-Generation Sequencing (NGS) reads according to the different cancer genomes, which can be mixed with specified proportions.

Usage

python $PYSUBSIMTREEPATH/pysubsimtree.py -c $CONFIG_PATH/ini.config -p $PREFIX

Configuration

A full demo is given in ./test. In Pysubsim-tree, Node labelled 1 is normal genome. Node labelled 1.1 is tumor subclone genome, Node 1 is parent node of Node 1.1.

./test/config/init.conf main configuration file

[pysubsimtree_settings]
#	Tumor evolution tree configuration file
SV_config_file=/media/d/github/pysubsimtree/test/config/variantTree.conf
#	reference genome
ref_fasta=/media/d/github/pysubsimtree/test/small.fa
#	dbsnp file
dbsnp=/media/d/github/pysubsimtree/test/small.vcf
#	number of germline snps
germline_num=2
#	ratio of heterozygou germline snps
hyp_rate=0.5
#	chromosome
chrome=chr1
# 	Tumor subpopulation fraction configuration file
population_fraction_config_file=/media/d/github/pysubsimtree/test/config/pf_config

./test/config/variantTree.conf Tumor evolution tree configuration file

# This is variant tree configuration file
# The sv configuration
#
# CNV
# Variant node label	Variant node type	Variant type	chrom	Length of CNVs	Copy number	Genotype	Number
1.1	SV	CNV	chr1	2	0	NONE	1
1.3.1	SV	CNV	chr1	2	0	NONE	1
1.3.1	SV	CNV	chr1	2	1	P	1
#1.1	SV	CNV	chr1	2	1	M	1
1.3.1	SV	CNV	chr1	2	2	PP	1
1.2	SV	CNV	chr1	2	2	MM	1
1.2.1	SV	CNV	chr1	2	3	PPM	1
#1.2.1	SV	CNV	chr1	2	3	PMM	1
#1.2.1	SV	CNV	chr1	2	3	MMM	1
#1.2.1	SV	CNV	chr1	2	4	PPPP	1
#1.2.1	SV	CNV	chr1	2	4	PPPM	1
#1.3	SV	CNV	chr1	2	4	PPMM	1
#1.3	SV	CNV	chr1	2	4	PMMM	1
1.3.1	SV	CNV	chr1	2	4	MMMM	1
#
# INVERTION
# Variant node label	Variant node type	Variant type	chrom	haplotype(Paternal or Maternal)	index of chromatid	Length	Genotype	Number
1.3.1	SV	INVERTION	chr1	P	0	4	2
#
# TANDEMDUP
# Variant node label	Variant node type	Variant type	chrom	haplotype(Paternal or Maternal)	index of chromatid	Length	Number
1.3.1	SV	TANDEMDUP	chr1	P	0	4	2	2
#
# INSERTION
# Variant node label	Variant node type	Variant type	chrom	haplotype(Paternal or Maternal)	index of chromatid	Length	Genotype	Number
1.3.1	SV	INSERTION	chr1	P	0	4	2
#
# DELETION
# Variant node label	Variant node type	Variant type	chrom	haplotype(Paternal or Maternal)	index of chromatid	Length	Genotype	Number
1.3.1	SV	DELETION	chr1	M	0	4	2
#
# TRANSLOCATION
# Variant node label	Variant node type	Variant type	chrom from	haplotype(Paternal or Maternal) from	index of chromatid from	Length	chrom to	haplotype(Paternal or Maternal) to	index of chromatid to	Number
1.3.1	SV	TRANSLOCATION	chr1	M	0	4	chr1	P	0	2
#
# SNV
# Variant node label	Variant node type	chrom	is heterozygous	is overlaped	number
1.3.1	SNV	chr1	FALSE	TRUE	2	2
1.3.1	SNV	chr1	TRUE	TRUE	2	2
1.3.1	SNV	chr1	FALSE	FALSE	2	2
#
# Aneuploidy event
# Variant node label	Variant node type	chrom 	ploidy number before	ploidy number after	ploidy status before	ploidy status after
1.3	PLOIDY	chr1	2	1	PM	PPM

./test/config/pf_config Tumor subpopulation fraction configuration file

#name	fraction
1	0.2
1.1	0.3
1.2	0.2
1.2.1	0.1
1.3	0.1
1.3.1	0.1