7.0 Enhancements In The Version 2.0
The
main enhancement in this version is the ability to do a fine-mapping run to follow
up a peak in a coarse scan. In addition to doing the fine-mapping run one can
also run simulations in this mode. A number of small enhancements have been
added as well, such as fast check for duplicates, support for PED files and
some extra output. A number of small bugs have been fixed as well.
In
detail the main enhancements are as follows:
1) A new
program baseprog allows the user to run the parameter file to make sure
the input files are valid, but does not do the MCMC calculation. See the example
parameter file parbaseprog which is part of the download. To run the
program type on the command line:
>>
baseprog –p parbaseprog or
>>./baseprog –p parbaseprog
p:
is a compulsory option, and in this case we have to specify the
parameter file parbaseprog.
To redirect the output in a file one
would type on the command line:
>>./baseprog –pv parbaseprog >
outbaseprog.dat&
2) Fine-mapping run capability including
simulations. A detailed write up is included in the next section.
3) Fast duplicate check: This is a quick check looking for duplicates
in the dataset, which is particularly useful in cases where we have a large
number
of samples, some of which maybe
duplicates. One can do this check by setting the parameter fastdup = YES in the parameter file.
4)
Checkindiv
check: This is a check for discarding individuals from the run, automatic in checkit mode.
5)
One can use
the physical position information to calculate or reset the genetic position,
useful for cases where user doesn’t have the genetic positions. This is
implemented using the parameter usephyspos.
6)
There is a
new pack mode which supported using the parameter packmode. By default the program sets this to YES, if number of
genotypes is greater than a certain number. The user should set this parameter
to YES if memory requirement seem large.
7)
User can
specify the high and low boundary values for log scores, through the parameters
hiclip and loclip.
8)
PED file
support, look at the documentation included.
9)
One can print
ancestry estimates for a particular SNP or Sample using the parameters:
pubxindname, pubx, pubxa and markername. For ex. If user wants to dump gammas
for a particular individual with internal individual index 2904 into a file
called gammaoutfile, one would specify the following parameters:
pubxname: gammaoutfile
pubx: 2904 -1
To
dump gammas for a particular marker:
pubxname: gammaoutfile
markername: fake-1:1672
Ex.
gamma output files for individual and marker.
10) We now print out information content for a SNP,
this is the rpower column in the output file.
11) The user
can print out the scores for all the markers in a file, to use this
functionality the user will need to specify the parameter localoutfilename.
12) New parameters with this release are given in the
accompanying table.
13) MAC Release: Experimental version not as well
tested is available for download.