You can download the program here
Or you can get the whole project and a zip file using this command: git clone https://github.com/pcingola/Askat.git (requires git installed).
You can take a look at some slides on the wrapper.
Requirements
- R : Make sure you have a resonably up to date version of R installed and availabe in you PATH.
- Java 1.6 : Most modern computers have Java installed.
- Fast-LMM : Pre-compiled versions of fast-Lmm can be found here (Linux and Windows).
WARNING: You should use relatively new version of Fast-LMM (e.g. version v1.09). - R Libraries: The ASKAT wrapper will tell you how to to install any missing R libraries.
Install
Just unzip the file and run the JAR by doing:
unzip askat.zip
Running the program
In order to run the program you need to go into the directory where you installed it an run the JAR file:
cd askat java -Xmx2G -jar Askat.jar [options] genotype
E.g.: To show a help message, just run the program without any parameters:
$ java -jar Askat.jar
ASKAT algorithm by Karim Oualkacha, optimized from N^3 to N^2 complexity by Stepan Grinek
Askat wrapper version 1.01 (build 2012-11-21), by Pablo Cingolani
Usage: java -jar Askat.jar [options] genotype
Options:
-b <num> : Number of SNPs used for calculating the kinship matrix. Default: 100000
-d : Debug mode (implies verbose)
-d1 : Debug mode. Perform only one sub-block calculation and stop
-i <bed> : BED file containing intervals to group SNPs. Default: none
-maxMaf : Maximum MAF (minor allelel frequency). Default: 1.0
-noDep : Do not perform dependency check.
-h : Show this help and exit.
-kin <type> : Kinship estimation type. Options {chr, avg, all, block}. Default: CHROMOSOME
-p <num> : Number of parallel processes. Default: 8
-pathBin <dir> : Path to binary programs (e.g. FastLmm). Default: './'.
-pathR <dir> : Path to R scripts (ASKAT scripts). Default './r/'.
-sb <num> : Number of SNPs used for calculating the ASKAT algorithm. Default: 20
-pACC <double> : Accuracy parameter for the p-value computation, default is 1e-9.
-v : Be verbose.
Some comments about the 'intervals' option
Whenever command line option '-i file.bed' is specified, Askat wrapper analyses all variants matching those intervals as a single block.
This means that variants are not subdivided into sub-blocks.
This is effectively like setting the subBlock parameter ('-sb') to infinity.
If a variant hits more than one interval, then it is analyzed on all intervals.
Although overlaping intervals are allowed, each interval is 'treated' as a unique block (this means that no statistical corrections are made in the model).
Running a full example
The genotype 'karim4k' is available for testing the program:
WARNING! By default Askat will try to use ALL the processors available in the computer. This will produce a significant slow down for all other users in the system.
The command line fo the example is:
$ java -Xmx1g -jar Askat.jar -v karim4k | tee karim4k.out
Note that we specified 1G of ram to be used by the program (parameter '-Xmx1G'), but in some other cases, more memory me be required.
The output looks like this:
00:00:00.001 ASKAT algorithm by Karim Oualkacha
00:00:00.004 Askat wrapper version 1.0 - epsilon 'almost 1.0' (build 2012-06-29), by Pablo Cingolani
00:00:00.004 Checking dependencies.
00:00:00.005 Checking dependency: Program 'R'
00:00:00.274 OK
00:00:00.275 Checking dependency: Program 'Rscript'
00:00:00.434 OK
00:00:00.434 Checking dependency: Program 'fastlmmc'
00:00:00.535 OK
00:00:00.536 Checking dependency: R library 'GenABEL'
00:00:02.099 Checking dependency: R library 'CompQuadForm'
00:00:02.387 Checking dependency: R library 'nFactors'
00:00:02.982 Checking dependency: R library 'MASS'
00:00:03.286 All dependencies found.
00:00:03.287 Running algorithm.
00:00:03.287 Creating blocks.
00:00:04.423 Creating block 'karim4k.block.1_100.tped'. Number of entries: 4000
00:00:04.511 Running block: karim4k.block.1_100.tped
00:00:04.512 Calculating kinship matrix for block: karim4k.block.1_100
00:00:23.197 Starting block: karim4k.block.1_100
00:00:23.284 Create batches.
File 'karim4k.block.1_100.tped' has 4000 lines.
Split up to 500 lines per batch.
00:00:23.287 Batch 1. Line 1. Creating batch : karim4k.block.1_100.1.askat
00:00:23.496 Batch 2. Line 501. Creating batch : karim4k.block.1_100.2.askat
00:00:23.673 Batch 3. Line 1001. Creating batch : karim4k.block.1_100.3.askat
00:00:23.845 Batch 4. Line 1501. Creating batch : karim4k.block.1_100.4.askat
00:00:24.019 Batch 5. Line 2001. Creating batch : karim4k.block.1_100.5.askat
00:00:24.190 Batch 6. Line 2501. Creating batch : karim4k.block.1_100.6.askat
00:00:24.365 Batch 7. Line 3001. Creating batch : karim4k.block.1_100.7.askat
00:00:24.538 Batch 8. Line 3501. Creating batch : karim4k.block.1_100.8.askat
00:01:33.747 ASKAT_RESUTS: Block: karim4k.block.1_100.1.askat Sub-Block: 1 - 20 chr:pos: 1:100 - 1:2000 Id: snp_1 - snp_20 p-value: 0.0006166988 Q: 38588.06 ...
00:01:35.749 ASKAT_RESUTS: Block: karim4k.block.1_100.2.askat Sub-Block: 1 - 20 chr:pos: 1:50100 - 1:52000 Id: snp_501 - snp_520 p-value: 0.6740977 Q: 10817.98 ...
00:01:36.750 ASKAT_RESUTS: Block: karim4k.block.1_100.3.askat Sub-Block: 1 - 20 chr:pos: 1:100100 - 1:102000 Id: snp_1001 - snp_1020 p-value: 4.551971e-07 Q: 57434.71 ...
00:01:36.750 ASKAT_RESUTS: Block: karim4k.block.1_100.8.askat Sub-Block: 1 - 20 chr:pos: 1:350100 - 1:352000 Id: snp_3501 - snp_3520 p-value: 0.6530349 Q: 11460.14 ...
00:01:37.751 ASKAT_RESUTS: Block: karim4k.block.1_100.4.askat Sub-Block: 1 - 20 chr:pos: 1:150100 - 1:152000 Id: snp_1501 - snp_1520 p-value: 0.9720287 Q: 5038.441 ...
00:01:37.751 ASKAT_RESUTS: Block: karim4k.block.1_100.6.askat Sub-Block: 1 - 20 chr:pos: 1:250100 - 1:252000 Id: snp_2501 - snp_2520 p-value: 0.1502854 Q: 18876.09 ...
00:01:38.752 ASKAT_RESUTS: Block: karim4k.block.1_100.5.askat Sub-Block: 1 - 20 chr:pos: 1:200100 - 1:202000 Id: snp_2001 - snp_2020 p-value: 1.340421e-06 Q: 54710.54 ...
00:01:38.753 ASKAT_RESUTS: Block: karim4k.block.1_100.7.askat Sub-Block: 1 - 20 chr:pos: 1:300100 - 1:302000 Id: snp_3001 - snp_3020 p-value: 1.385112e-05 Q: 48982.58 ...
00:02:22.786 ASKAT_RESUTS: Block: karim4k.block.1_100.1.askat Sub-Block: 21 - 40 chr:pos: 1:2100 - 1:4000 Id: snp_21 - snp_40 p-value: 0.2958578 Q: 16597.14 ...
00:02:25.788 ASKAT_RESUTS: Block: karim4k.block.1_100.2.askat Sub-Block: 21 - 40 chr:pos: 1:52100 - 1:54000 Id: snp_521 - snp_540 p-value: 0.7232833 Q: 10029.99 ...
00:02:26.789 ASKAT_RESUTS: Block: karim4k.block.1_100.3.askat Sub-Block: 21 - 40 chr:pos: 1:102100 - 1:104000 Id: snp_1021 - snp_1040 p-value: 0.01380279 Q: 28006.57 ...
00:02:27.790 ASKAT_RESUTS: Block: karim4k.block.1_100.8.askat Sub-Block: 21 - 40 chr:pos: 1:352100 - 1:354000 Id: snp_3521 - snp_3540 p-value: 0.001698173 Q: 37035.88 ...
00:02:28.791 ASKAT_RESUTS: Block: karim4k.block.1_100.4.askat Sub-Block: 21 - 40 chr:pos: 1:152100 - 1:154000 Id: snp_1521 - snp_1540 p-value: 0.1902052 Q: 18511.61 ...
00:02:28.791 ASKAT_RESUTS: Block: karim4k.block.1_100.5.askat Sub-Block: 21 - 40 chr:pos: 1:202100 - 1:204000 Id: snp_2021 - snp_2040 p-value: 0.6349479 Q: 10588.31 ...
00:02:28.792 ASKAT_RESUTS: Block: karim4k.block.1_100.6.askat Sub-Block: 21 - 40 chr:pos: 1:252100 - 1:254000 Id: snp_2521 - snp_2540 p-value: 0.8626755 Q: 8638.986 ...
00:02:28.792 ASKAT_RESUTS: Block: karim4k.block.1_100.7.askat Sub-Block: 21 - 40 chr:pos: 1:302100 - 1:304000 Id: snp_3021 - snp_3040 p-value: 0.3494253 Q: 15464.29 ...
...
...
...
Input data formats
ASKAT wrapper requires the input data to be formatted in two file: TFAM and TPED format (for details, see PLINK software package).
- TFAM: This is the typical "Transposed FAM". TFAM file have individual and family information, where one row is an individual.
The columns are:- Family ID
- Individual ID
- Paternal ID
- Maternal ID
- Sex (1=male; 2=female; other=unknown)
- Phenotype
- TPED: This is a "Transposed PED". TPED file have SNP information, where one row is a SNP (for all samples).
The columns are:- chromosome (1-22, X, Y or 0 if unplaced)
- rs# or snp identifier
- Genetic distance (morgans)
- Base-pair position (bp units)
- Columns 5 and on: Genotype informaton (two bases per sample, assuming )
E.g.: TFAM data:
1 1_1 0 0 1 4.91995 1 1_2 0 0 2 7.14442 1 1_3 1_1 1_2 2 5.26482 2 2_1 0 0 1 2.87951 2 2_2 0 0 2 1.52721 2 2_3 2_1 2_2 2 2.45878 2 2_4 2_1 2_2 1 2.59495 3 3_1 0 0 1 2.17923 3 3_2 0 0 2 3.91823 3 3_3 3_1 3_2 1 2.55475
E.g.: TPED data (long lines have been truncated):
1 snp_1 0 100 A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A ... 1 snp_2 0 200 A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A ... 1 snp_3 0 300 A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A ... 1 snp_4 0 400 A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A ... 1 snp_5 0 500 A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A ... 1 snp_6 0 600 A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A T T A A T A T A T A T A A A T A A A A A T A T A A A ... 1 snp_7 0 700 A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A ... 1 snp_8 0 800 A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A ... 1 snp_9 0 900 A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A T A A A A A T A T A A A A A ...