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.