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* Source code can be downloaded in the following
* Source code can be downloaded in the following
[[Media:LINUX_famrvtest.2.2.tgz|Source for '''LINUX''']]
[[Media:LINUX_famrvtest.2.4.tgz|Source for '''LINUX''']]
[[Media:MAC_famrvtest.2.2.tgz|Source for '''MAC''']]
[[Media:MAC_famrvtest.2.4.tgz|Source for '''MAC''']]
[[Media:MINGW_famrvtest.2.2.tgz|Source for '''MINGW''']]
[[Media:MINGW_famrvtest.2.4.tgz|Source for '''MINGW''']]
[[Media:CYGWIN64_famrvtest.2.2.tgz|Source for '''CYGWIN64''']]
[[Media:CYGWIN64_famrvtest.2.4.tgz|Source for '''CYGWIN64''']]
* Executable can be downloaded in the following:
* Executable can be downloaded in the following:
[[Media:Linux_binary.tar.gz |Executable for '''LINUX''']]
[[Media:Famrvtest.2.4.linux.executable.tgz |Executable for '''LINUX''']]
=== How to Compile ===
=== How to Compile ===
* Save it to your local path and decompress using the following command:
* Save it to your local path and decompress using the following command:
tar xvzf Linux_famRvTest.2.2.tgz
tar xvzf LINUX_famrvtest.2.4.tgz
* Go to promp>famrvtest and type the following command to compile:
* Go to promp>famrvtest and type the following command to compile:
make -j 5
make
=== How to Execute ===
=== How to Execute ===
=== PED and DAT Files ===
=== PED and DAT Files ===
* When PED file has genotypes saved, there is no need for a VCF file as input.
* When PED file has genotypes saved, there is no need for a VCF file as input.
* '''famrvtest''' takes PED/DAT file in [http://www.sph.umich.edu/csg/abecasis/Merlin/index.html|'''Merlin'''] format. Please refer to [http://www.sph.umich.edu/csg/abecasis/merlin/tour/input_files.html PED/DAT format description] for details.
* '''famrvtest''' takes PED/DAT file in [http://www.sph.umich.edu/csg/abecasis/Merlin/index.html '''Merlin'''] format. Please refer to [http://sph.umich.edu/csg/abecasis/merlin/tour/input_files.html PED/DAT format description] for details.
* An example PED file is in the following:
* An example PED file is in the following:
1 1 0 0 1 1.5 1 23 A A A A A A A A A A
1 1 0 0 1 1.5 1 23 A A A A A A A A A A
tabix -p vcf -f input.vcf.gz ## this command will generate input.vcf.gz.tbi
tabix -p vcf -f input.vcf.gz ## this command will generate input.vcf.gz.tbi
* Even with the presence of VCF file, PED/DAT files are still needed for covariates and phenotypes.
* Even with the presence of VCF file, PED/DAT files are still needed for covariates and phenotypes.
=== Group File for Gene-level Tests===
* Grouping methods are only necessary for gene-level tests.
* With --groupFile option, you can specify particular set of variants to be grouped for burden tests.
* The group file must be a tab or space delimited file in the following format:
GROUP_ID MARKER1_ID MARKER2_ID MARKER3_ID ...
* MARKER_ID must be in the following format:
CHR:POS:ALLELE1:ALLELE2
* An example group file is:
PLEKHN1 1:901922:G:A 1:901923:C:A 1:902088:G:A 1:902128:C:T 1:902133:C:G 1:902176:C:T 1:905669:C:G
HES4 1:934735:A:C 1:934770:G:A 1:934801:C:T 1:935085:G:A 1:935089:C:G
* '''Version 2.4 and later allow variants from different chromosomes to be grouped for testing. This might be useful for pathway analysis.'''
* '''Note: any variants that have different alleles from listed in group file will be excluded from gene-level tests.'''
== Example Command Line ==
== Example Command Line ==
* Released version 2.0, a faster version and added family-based single variant permutation test. (7/14/2014)
* Released version 2.0, a faster version and added family-based single variant permutation test. (7/14/2014)
* Released version 2.2, a bug fixed which causes single variant test can not be run alone. (7/15/2014)
* Released version 2.2, a bug fixed which causes single variant test can not be run alone. (7/15/2014)
* Uploaded new source code package for version2.2, with updated makefiles. (8/4/14)
* Released version 2.3. Fixed a bug which causes compiling error (not finding the correct makefile). (8/20/14)
* Released version 2.4. Enable analyzing pathways where variants from different chromosomes can be grouped. (9/27/2014)
