Under csh:
   set d = ./2012-03-29_ShotGun
   set hf = $d/data/canHap/chrs44880.1.canHap.gz
   set pf = $d/data/simp_pos/EU.1.pos
   $d/bin/ShotGun -h $hf -p $pf -n 60 -d 6 -o n60.depth6

Under bash:
   d=./2012-03-29_ShotGun
   hf=$d/data/canHap/chrs44880.1.canHap.gz
   pf=$d/data/simp_pos/EU.1.pos
   $d/bin/ShotGun -h $hf -p $pf -n 60 -d 6 -o n60.depth6

The command line above generates average 6X sequencing data for 60 individuals.

ShotGunOnly

Full Documentation for the options:

--hapfile[-h] : Required input haplotype file
example w/ 20 chromosomes at 50 markers
--posfile[-p] : Required input position file
example for 50 markers
--errorfile : Optional input cycle-specific error file
example for 35-base reads
--seed : Random seed, integer, default = 12345
--readlength[-l] : Read Length, positive integer, default = 100
--minwts : Recommend using --alpha (below) instead.
--BeginningPosition[b] : Start Position, positive number, default = 1.0
--EndingPosition[e] : End Position, positive number, default = 100000.0
--sequencableProportion: Sequencable Proportion, default = 1.0
--alpha[a] : False Positive Rate, default = 1e-3
1e-3 corresponds to 100 false positives in a 100Kb region
--shape[s] : Shape Parameter for Gamma Mixture.
Default = 4.0, also see --negativeBinomial.
Smaller value => more severe over-dispersion compared with Poisson.
--numIndividuals[n] : Number of individuals to be sequenced
positive integer, default = 100
--depth[d] : Average Sequencing Depth per Individual.
--erate : Average Sequencing Error Rate, ignored if --errorfile provided.
--allbps : Output Information for ALL Base Pairs,
regardless of evidence for being polomorphic.
--negativeBinomial : Depths follow Negative Binomial distribution.
Implemented as a Gamma mixture of Poisson's.
Shape parameter of Gamma specified by --shape.
--trueped : Output true genotype information at detected markers.
--numReplications : #Replicates to determine polymorphism score threshold.
--prefix : Output prefix.

How To Run

ShotGun+DesignPlanner

CommandLine Options Output Interpretation OutputFields

Command Line Example:

Under csh:
   set d = ./2012-03-29_ShotGun
   cd $d
   ./DesignPlanner.csh 0

Under bash:
   d=./2012-03-29_ShotGun
   cd $d
   ./DesignPlanner.csh 0

     The command line above will generate effective sample size estimate for each MAF category for the default setting: 30 individuals sequenced at depth 5X (you can change the parameters by changing the 26th and 28th line in the shell script), with a ShotGun false positve rate of ~1/1,000 (that is, ~100 false positive SNPs in each 100Kb region).
     Note that the 0 at the end of the command line is for setting warning option. By default warning = 1, which means the program will STOP for warning.
     See example screen output after running a similar command line (60 individuals at depth 2X).

ShotGun+DesignPlanner

Options:

Options are specified in DesignPlanner.csh. You will need to modify the codes inside the shell script, in the "SET PARAMETERS" sections at the beginning of the shell script. The following options are available:

n : #individuals
t : depth
alpha: false positive rate (see ShotGunDocumentation)
erate: Average Sequencing Error Rate (see ShotGunDocumentation)
st : --states for thunder
larger is better at the cost for quadratically increased computing time
rd : --rounds for thunder
larger is better at the cost for linearly increased computing time

ShotGun+DesignPlanner