10.1
Download instructions for the program
Follow
these steps to download and install ANCESTRYMAP on your computer:
1.
Go to http://genepath.med.harvard.edu/~reich
2.
Click on:
Download for UNIX or Linux or MAC for
the source code
3.
Make sure to
rename the downloaded file to ancestrymap.tar.gz, since the download process
sometimes renames it otherwise.
4.
Decompress
the file using gzip –d ancestrymap.tar.gz, and you should now see
ancestrymap.tar
5.
Unarchive
this file using tar –xvf ancestrymap.tar. This will create a directory called ancestrymap, and the following directory
structure under it:
examplesfiles/
src/
bin/
README file
In
the examplefiles directory we have
the following files:
Parmeter
Files:
§
paramfile: In the format of parameter
file for ancestrymap, with additional parameters that are new in
Version 2.0
§
parmono: In the format of parameter
file for cntmono
§
param0, param1, param2: Parameter files for ancestrymap, discussed later in this section
§
parsim: Parameter file for ancestrymap when running simulations
§
parsim2d:
Parameter file for ancestrymap when
running fine-mapping simulations
§
paramped:
Parameter file for ancestrymap when
using PED files
§
par:8001-par:8009
: Parameter files for fine-mapping runs
as generated by running the script mkfine.
§
Example files
as used by convertf executable, look at the relevant documentation for details
Input
Data Files:
§
indiv.dat: individual input file for ancestrymap
§
indiv1.dat : Individual file for ancestrymap
with one samples set to Ignore
§
geno.dat:
genotype input file for ancestrymap
§
snpcnts:
marker input file for ancestrymap
§
badsnps: input file for ancestrymap with markers that need to be removed from the analysis
§
snps: marker input file for cntmono or ancestrymap
§
aflist, eurlist: Ancestry files for cntmono
The
genotype and individual files in this directory were generated by running
simulations, and the marker files correspond to data reported in the Smith
et al paper.
Output
Files:
§
out2.dat Output file generated by running ancestrymap using paramfile
§
out0.dat: Output file generated by running ancestrymap
using param0
§
out1.dat: Output file generated by running ancestrymap using param1
§
outsim2d.dat
: Output file generated by running ancestrymap
using parsim2d
§
admckout.dat: Ouput file generated by running admcheck
on out1.dat
§
indjunk:
Output file with detailed individual data created by running ancestrymap using
param0
§
snpjunk:
Output file with detailed marker data created by running ancestrymap using
param0
§
Fine-mapping Run Output Files:
1.
badlist1,
framelist1: Output files generated by mkfine
script
2.
badlist:8001-badlist:8009:
Bad marker files generated by mkfine
for each fine-mapping run
3.
xx:8001-xx:8009:
Output file for each fine-mapping run
§
outfiles/: This is a directory which contains the output
files mentioned in Section 6, and ancestry
estimates for various markers considered in the fine-mapping run
(gams:8001-gams:8009).
bin/ has the
following executables:
§
cntmono
§
ancestrymap
§
baseprog
§
admcheck:
A perl script which is used to extract the top “bad” markers
§
mkfine: A
perl script which is used to kick-off the fine-mapping runs
§
parfine.temp : A accompanying template parameter file needed by the mkfine script
§
addcol, uniqit: Helper perl scripts needed by mkfine
src/ has the C
source code for making the ancestrymap,
cntmono, baseprog, convertf executables, the library nicklib.a and a makefile
called Makefile. The makefile can be sued to make just the individual
executables, or just the library or all together. This also has the following
directories:
§
smartinclude/ has header files which are needed by the source code, users should
not delete these files to ensure proper compilation of the code.
§
smarttables/ is needed by the source code.
§
nicksrc/: nicklib source code