000001 ! batch item number {only REQUIRED batch item}
1 ! analysis: 1=Haplo; 2=LOD; 3=NPL; 4=IBD; 5=Mistyping
000002 ! batch item number
1 ! integer label for this run of the program
000003 ! batch item number
Pedigree Analysis by SimWalk
000004 ! batch item number
N ! continuation of a previous job?
000005 ! batch item number
N ! run silently, i.e., no screen output?
000009 ! batch item number
MAP.DAT ! name of map file
000010 ! batch item number
LOCUS.DAT ! name of locus file
000011 ! batch item number
PEDIGREE.DAT ! name of pedigree file
000012 ! batch item number
F ! symbol for female (case insensitive)
M ! symbol for male (case insensitive)
000013 ! batch item number
Y ! is trait listed in locus and pedigree files?
1.0 ! proportion of pedigrees linked to trait locus; optional
000016 ! batch item number
2 ! label indicating an affected individual
000017 ! batch item number
0 ! affected status in:0=>trait locus; n>0 =>nth quant var
000018 ! batch item number
0 ! number of quantitative variables in pedigree
000019 ! batch item number {only for location scores}
! name of penetrance file; blank implies no file
000020 ! batch item number
1000 ! number of pedigrees sampled for each input pedigree
000021 ! batch item number {for simulated annealing}
1 ! number of parallel runs to perform
000022 ! batch item number {for simulated annealing}
100.0 ! 'temperature' at beginning of simulated annealing
000023 ! batch item number {for simulated annealing}
0.99 ! factor by which the 'temperature' changes
000024 ! batch item number {for simulated annealing}
800 ! number of 'temperature' changes
000025 ! batch item number {for simulated annealing}
0 ! number of pre-simulated annealing steps
000026 ! batch item number
64 ! maximum number of attempts to find a legal state
000029 ! batch item number
1000 ! min. # of steps between sampled peds in sim. annealing
1000 ! min. # of steps between sampled peds in MCMC procedure
000030 ! batch item number
10 ! factor for number of steps in sim. annealing
10 ! factor for number of steps in MCMC procedure
000031 ! batch item number
2.00 ! mean # of transitions/step in sim. annealing
2.00 ! mean # of transitions/step in MCMC procedure
000032 ! batch item number
10 ! weight for untyped people in sim. annealing
10 ! weight for untyped people in MCMC procedure
000033 ! batch item number
0.50 ! weight for neighbor-pivot in sim. annealing
0.50 ! weight for neighbor-pivot in MCMC procedure
000034 ! batch item number
0.25 ! freq of transition type 2 in sim. annealing
0.25 ! freq of transition type 2 in MCMC procedure
000035 ! batch item number
0 ! number of steps between 'free' runs
000036 ! batch item number
27713 ! random positive integer < 30000
2321 ! random positive integer < 30000
18777 ! random positive integer < 30000
000038 ! batch item number
! name of file containing precomputed NPL statistics
000039 ! batch item number
ALL ! which IBD analysis files to output: IBD, KIN or ALL
000040 ! batch item number
N ! create the INPED-nn.mmm files?
000041 ! batch item number {only for location scores}
N ! create the SCORE-nn.mmm files?
000042 ! batch item number
0.50 ! threshold for significance of mistyping
000043 ! batch item number {only for haplotyping}
Y ! create the haplotype export files?
000044 ! batch item number {only for haplotyping}
0 ! haplotype threshold for rerunning a pedigree
0 ! recombination threshold for rerunning a pedigree
000045 ! batch item number {only for haplotyping}
0.85 ! step count threshold for rerunning a pedigree
000046 ! batch item number {only for haplotyping}
N ! haplotypes displayed vertically?
N ! haplotypes displayed using founder-source label?
N ! allele specified even when no information available?
000047 ! batch item number
N ! output pedigrees in Linkage-format?
000048 ! batch item number {only for NPL statistics}
1000 ! number of unconditional simulations for p-value
000049 ! batch item number
3 ! points within each marker interval; -1 => use grid
1.0 ! grid increment in cM at which values are computed
000050 ! batch item number signifying end of data
The in-line descriptions shown above are by necessity very brief. For more complete descriptions, please see the BATCH2.DAT format file.
The only commonly altered batch items are #1-16.
The order in which the batch items are listed is arbitrary, except that batch item #50 signifies the end of the data and the rest of the file is then ignored.
Each batch item in this example file specifies the default values and may therefore be omitted, except for batch item #1, which is required and has no default value.
It is highly recommended that one use these default values unless there is a compelling reason to change them. The easiest method to insure one is using the default values is to omit the corresponding batch item from the BATCH2.DAT file.
With this in mind, the entire above example is equivalent to a file containing only the following 3 lines:
________________________<start of file>______________________________________
000001
1
________________________<end of file>________________________________________