chenyangkang / PooledPSMC

Auto-PSMC with pooled individuals

PooledPSMC

Auto-PSMC with pooled individuals

usage

input files

1. A bam_list file that contain all the bam file path to the individuals. For example:

/home/user1/project1/indiv1.bam
/home/user1/project1/indiv2.bam
/home/user1/project1/indiv3.bam
/home/user1/project1/indiv4.bam

2. A project name list with all project/individual names corresponding to the bam file. For example:

indiv1
indiv2
indiv3
indiv4

3. Reference genome

to run:

simply call python PooledPSMC.py (or python PooledPSMC.py -h to see the help)

Make sure you have

samtools
bcftools
fq2psmcfa
psmc
splitfa
vcfutils.pl
psmc_plot.pl
bamtools
pandas
matplotlib
numpy

in your environment.