README.md
August 26, 2016 ยท View on GitHub
##Citing QCAT QCAT: testing causality of variants using only summary association statistics, Donghyung Lee; Tim B. Bigdeli; Vladimir I. Vladimirov; Ayman H. Fanous; Silviu-Alin Bacanu; submitted.
##Acknowledgement This work is supported by the National Institutes of Health with grants R25DA26119, R21MH100560, R21AA022717 and P50AA022537.
##Download QCATMIX The current release (Version 0.1.0) of QCATMIX 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 QCAT/QCATMIX are available upon request (dustorm_at_gmail_dot_com)
| Direct download link | Version | Release Date |
|---|---|---|
| QCATMIX for a Linux user | v1.0.0 | 08/25/2016 |
##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 QCATMIX. 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 |
##Options
| Option | Short Flag | Parameter | Default | Description |
|---|---|---|---|---|
| --version | -v | none | none | Prints version information. |
| --help | -h | none | none | Outputs a full description of all QCAT/QCATMIX options. |
| --local | none | none | none | Execute QCAT local test. |
| --reference | -r | filename | none | The filename of the reference population data. |
| --referenceIndex | -i | filename | none | The filename of the reference population index data. |
| --referenceInfo | none | filename | none | The filename of the reference panel information. |
| --output | -o | filename | out.qcat | The filename of QCAT/QCATMIX output |
| --chromosome | -c | integer or string | 1.0 | Chromosome number (or chromosome number and arm, e.g., 1q, 22p) |
| --startBp | -non | decimal | none | The start position of prediction window. |
| --endBp | -non | decimal | none | The end position of prediction window. |
| --windowSize | -n | decimal | 1.0 | The size of the prediction window (Mb). |
| --wingSize | -m | decimal | 0.5 | The size of the wing padded on the left and right of the prediction window (Mb). |
| --populationWeight | -w | filename | none | The filename of the population weight data. |