Simulator of modern human and Neanderthal demography
Dependencies: numpy, pandas, msprime, jupyter.
$ ./demography.py --help
usage: demography.py [-h] [--eurA start,duration,rate1,rate2]
[--eurB start,duration,rate1,rate2]
[--afr start,duration,rate1,rate2]
[--neand start,duration,rate1,rate2]
[--Ne-nonafr NE_NONAFR] [--Ne-afr NE_AFR] --seq-len
SEQ_LEN
(--eur-ages EUR_AGES [EUR_AGES ...] | --neur NEUR)
[--nasn NASN] [--nafrA NAFRA] [--nafrB NAFRB]
[--introgression from-to] [--snps]
[--stats {true_neand,asc_neand,indirect,direct,afr_f4} [{true_neand,asc_neand,indirect,direct,afr_f4} ...]]
[--output-prefix FILE] [--debug]
optional arguments:
-h, --help show this help message and exit
--eurA start,duration,rate1,rate2
EUR <-> AFR_A geneflow
--eurB start,duration,rate1,rate2
EUR <-> AFR_B geneflow
--afr start,duration,rate1,rate2
AFR_A <-> AFR_B geneflow
--neand start,duration,rate1,rate2
nonAfr <-> Neanderthal geneflow
--Ne-nonafr NE_NONAFR
--Ne-afr NE_AFR
--seq-len SEQ_LEN Sequence length
--eur-ages EUR_AGES [EUR_AGES ...]
Ages of European samples [years BP]
--neur NEUR Number of European chromosomes to simulate
--nasn NASN Number of Asian chromosomes to simulate
--nafrA NAFRA Number of AfrA chromosomes to simulate
--nafrB NAFRB Number of AfrB chromosomes to simulate
--introgression from-to
Pair of populations for introgression detection
--snps Save all SNPs to a file
--stats {true_neand,asc_neand,indirect,direct,afr_f4} [{true_neand,asc_neand,indirect,direct,afr_f4} ...]
Which statistics to calculate?
--output-prefix FILE Prefix of output files
--debug Debug info