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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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| GROUP_ID MARKER1_ID MARKER2_ID MARKER3_ID ... | | GROUP_ID MARKER1_ID MARKER2_ID MARKER3_ID ... |
| * MARKER_ID must be in the following format: | | * MARKER_ID must be in the following format: |
− | CHR:POS_ALLELE1/ALLELE2 | + | CHR:POS:ALLELE1:ALLELE2 |
| * An example group file is: | | * 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 | + | 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 | + | 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.''' |
− | ===Group Info from Annotated VCF File===
| + | * '''Note: any variants that have different alleles from listed in group file will be excluded from gene-level tests.''' |
− | If --groupFile option is '''NOT''' specified, ''''famrvtest''' will look for an annotated vcf file as blue print for variants to group. Users are also allowed to generate a vcf file based on the superset of variants from pooled samples, and annotate outside RAREMETAL. Then, annotated vcf file can be used as input for RAREMETAL for gene-level meta-analysis, or group files can be generated based on the annotated vcf file. Detailed description of these options are [[Rare-Metal#Group_Rare_Variants_from_Annotated_VCF|'''available''']].
| |
| | | |
| == Example Command Line == | | == Example Command Line == |
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| * 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) | | * 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) |