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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 | | make |
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| === 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 |
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| 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 == |
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| * 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) |