Extends https://github.com/nlapier2/MsCAVIAR/
The majority of PIPSORT development was done on a fork. We have moved the code to this new repo. For prior commit history, please see https://github.com/TaraMirmira/MsCAVIAR
git clone https://github.com/CAST-genomics/pipsort.git
cd pipsort/
make
The -l and -z arguments, as can be seen in the tests/example/ folder, list the files with the LD matrix and Z scores for the SNPs in the locus, respectively. The file paths should be given either as absolute file paths or relative paths to the current directory.
For each study, the number of lines in the LD file should match the number of lines in the Z file. The number of lines across studies need not match to allow for the sets of variants to differ across studies.
The Z files should contain two tab-separated columns. The first column should be the variant name and the second should be the Z-score for that variant. See the files in the tests/example/ folder for examples of these file types.
-m To accommodate different sets of variants across studies, PIPSORT needs a variant map. For two studies, this is a 3-column comma-separated file. The first column is the variant name. The second column is the index of the variant in the first study (or -1 if it is not present in that study). The third column is the index of the variant in the second study (or -1 if it is not present). We provide helper scripts for formatting summary and statistics and constructing this map in utils/. Additionally we provide a script (get_pipsort_inputs.sh) that takes in two GWAS summary statistic files in PLINK format and outputs the variant map and summary statistics formatted appropriately for use by PIPSORT.
The -n argument specifies the population size for each study, comma-separated. Again, this should be the same number of studies and in the same order as was given by the -l and -z arguments.
The -o argument is simply the output name prefix for the PIPSORT output files.
-c controls the maximum number of causal SNPs allowed at a locus; the default is 3.
The other command line options are listed below. We do not recommend changing -g or -s for most users.
-t controls the heterogeneity between the studies; in other words, the variance in the effect sizes of causal SNPs not accounted for by sample size imbalance. The default is 0.52.
-r RHO, --rho-prob=RHO set $rho$ probability (default 0.95)
-g GAMMA, --gamma set $gamma$ the prior of a SNP being causal (default 0.01)
-c causal set the maximum number of causal SNPs (default 3)
-t TAU_SQR, --tau_sqr=TAU_SQR set the heterogeneity (t^2) across studies, default is 0.52
-s SIGMA_G_SQR, --sigma_g_squared=SIGMA_G_SQR set the NCP variance for the smallest study, default is 5.2
An example for running PIPSORT can be found in tests/example. All necessary files are provided as well as expected output files. The example can be run with run_example.sh.
There are a few probabilities computed after PIPSORT runs: global PIPs and not shared PIPs. Scripts for computing these are provided in utils/ and example usage is provided in run_example.sh.