##Citing JEPEGMIX JEPEGMIX: a summary statistics based tool for gene-level joint testing of functional variants, Donghyung Lee; Vernell S. Williamson; Tim B. Bigdeli; Brien P. Riley; Bradley T. Webb; Ayman H. Fanous; Kenneth S. Kendler; Vladimir I. Vladimirov; Silviu-Alin Bacanu; Bioinformatics (2016) Jan 15; 32(2):295-7. doi:10.1093/bioinformatics/btv567.
##Acknowledgement This work is supported by the National Institutes of Health with grants R25DA26119, R21MH100560, R21AA022717 and P50AA022537.
##Download JEPEGMIX The current release (Version 0.1.0) of JEPEGMIX is for a Linux user. The pre-compiled executables for other operating systems (e.g., Windows, MacOS) will be available soon. The latest source codes of JEPEGMIX are available upon request (dustorm_at_gmail_dot_com)
| Direct download link | Version | Release Date |
|---|---|---|
| JEPEGMIX for a Linux user | v0.1.0 | 07/13/2015 |
##Download Reference Panels
| Direct download link | Number of Samples | Number of populations | NCBI build | Release Date | Note |
|---|---|---|---|---|---|
| 1000 Genomes Phase1 Release3 | 1092 | 14 | build 37 (hg19) | Nov. 23 2010 | Includes chr1-chr22 |
Here are the 1000 Genome population abbreviations used by JEPEGMIX. AFR is an abbreviation for African; AMR for admixed American; ASN for East Asian; EUR for European.
| Population Abbreviation | Number of Subjects | Super Population | Population Description |
|---|---|---|---|
| ASW | 61 | AFR | African Ancestry in Southwest US |
| CEU | 85 | EUR | Utah residents (CEPH) with Northern and Western European ancestry |
| CHB | 97 | ASN | Han Chinese in Beijing, China |
| CHS | 100 | ASN | Southern Han Chinese |
| CLM | 60 | AMR | Colombian in Medellin, Colombia |
| FIN | 93 | EUR | Finnish in Finland |
| GBR | 89 | EUR | British in England and Scotlant |
| IBS | 14 | EUR | Iberian populations in Spain |
| JPT | 89 | ASN | Japanese in Tokyo, Japan |
| LWK | 97 | AFR | Luhya in Wenbuye, Kenya |
| MXL | 66 | AMR | Mexican Ancestry from Los Angeles, USA |
| PUR | 55 | AMR | Puerto Rican in Puerto Rico |
| TSI | 98 | EUR | Toscani in Italia |
| YRI | 88 | AFR | Yoruba in Ibadan, Nigeria |
##Download SNP Annotation Data
| Direct download link | Version | Release Date |
|---|---|---|
| SNP annotations | v0.2.0 | 11/20/2014 |
##JEPEGMIX Input File Format
###When study allele frequency information is available JEPEGMIX takes as input a plain text file with rows and columns denoting SNPs and variables, respectively. The first line of the input file should be column names/headers. Data entries on each line should be separated by white space. The file should contain eight columns: 1) rsid (SNP ID), 2) chr (chromosome number), 3) bp (base pair position), 4) a1 (reference allele), 5) a2 (alternative allele), 6) z (normally distributed GWAS/meta-analysis summary statistic, i.e. two-tailed Z-score), 7) info (imputation information) and 8) af1 (cohort reference allele frequency (RAF)). JEPEGMIX does not require the input data to be sorted in ascending order by chromosome number and base pair position or SNP ID. Here is a sample JEPEGMIX input file.
rsid chr bp a1 a2 z info af1
rs1000109 9 117908733 C T -0.714464 0.890 0.384
rs10001109 4 44904653 C T 0.721919 0.731 0.198
rs1000112 22 28273339 C G -0.583666 0.445 0.042
rs10001127 4 130547376 T C 0.069329 0.999 0.210
rs1000113 5 150240076 T C -1.447288 1.0 0.189
###When study allele frequency information is not available Genome-wide association studies/meta-analyses typically do not provide study allele frequency information due to privacy issues. However, information about ethnic proportion of the study samples is usually available from the publications. By using the prior ethnic information, users can run JEPEGMIX for association summary data lacking allele frequency information. In this case, JEPEGMIX does not require study allele frequency information (the column ‘af1’) in the input file, but additionally JEPEGMIX needs one more input text file (population weight file) specifying ethnic proportion of the study samples. Here is a sample JEPEGMIX input file with 5 SNPs, which should be used when allele frequency information is not available.
rsid chr bp a1 a2 z info
rs1000109 9 117908733 C T -0.714464 0.890
rs10001109 4 44904653 C T 0.721919 0.731
rs1000112 22 28273339 C G -0.583666 0.445
rs10001127 4 130547376 T C 0.069329 0.999
rs1000113 5 150240076 T C -1.447288 1.0
Note: If the input summary data comes a different genome assembly (e.g. NCBI build 36 (hg18)) than NCBI build 37 (hg19), it needs to be converted by the user to NCBI build 37 (hg19) using a software, called liftover, from UCSC.
Here is a sample JEPEGMIX population weight file, which is needed when cohort allele frequency information is not available.
pop wgt
ASW 0.1
GBR 0.3
FIN 0.2
CEU 0.25
IBS 0.15
The first line of the population weight file should be column names/headers. The file should contain two columns: 1) pop (population abbreviation) and 2) wgt (population proportion). The columns of data should be separated by white space. The weight file name should be specified with the ‘--populationWeight’ option.
##JEPEGMIX output file format
The JEPEGMIX/JEPEG output file has nine columns: 1) gene name (geneid), 2) chi-square test statistic value (chisq), 3) degrees of freedom (df), 4) JEPEGMIX p-value (jepegmix_pval), 5) number of functional SNPs associated with gene (num_snp), 6) top functional category (top_categ), 7) top category p-value (top_categ_pval), 8) top functional SNP ID (top_snp) and 9) top SNP p-value (top_snp_pval). The first line of the output file is column names/headers. Here is a sample JEPEGMIX(JEPEG) output file, with 5 genes:
geneid chisq df jepeg_pval num_snp top_categ top_categ_pval top_snp top_snp_pval
FCGR3B 14.926 1 1.80E-05 2 PFS 1.10E-04 rs5030738 5.08E-05
CSPG4P2Y 14.774 2 3.29E-05 5 TRN 1.21E-04 rs10828664 5.55E-05
SLC7A7 19.902 3 3.40E-05 33 TRN 3.51E-04 rs9304810 1.07E-03
EDARADD 13.957 2 3.93E-05 2 PFS 1.86E-04 rs966365 7.80E-06
FAM71D 13.026 1 4.34E-05 26 TAR 3.07E-04 rs45515505 1.53E-04
##Options
| Option | Short Flag | Parameter | Default | Description |
|---|---|---|---|---|
| --version | -v | none | none | Prints version information. |
| --help | -h | none | none | Outputs a full description of all JEPEGMIX options. |
| --impute | none | none | none | Imputes summary statistics of unmeasured functional SNPs using DISTMIX before JEPEGMIX analysis. |
| --reference | -r | filename | none | The filename of the reference population data. |
| --referenceIndex | -i | filename | none | The filename of the reference population index data. |
| --annotation | -a | filename | none | The filename of the SNP annotation data set. |
| --output | -o | filename | out.jepegmix | The filename of JEPEGMIX(JEPEG) output |
| --windowSize | -n | decimal | 1.0 | The size of the DISTMIX prediction window (Mb). |
| --wingSize | -m | decimal | 0.5 | The size of the wing padded on the left and right of the DISTMIX prediction window (Mb). |
| --populationWeight | -w | filename | none | The filename of the population weight data. |
| --impInfoCutoff | none | decimal | 0.3 | The imputation information cutoff. |