First version used in the original method manuscript

Create a tag to obtain a DOI for the method manuscript.

1.0.9

A stable tested on DNAnexus for benchmarks on the exome-wide association tests using UK Biobank 450k WES data

v1.0.4

Bugs fixed:

Fix the issue when SKAT-O is performed with no weights applied to markers and one or more groups have no markers. error message "Error in if (abs(q - m1)/sqrt(var1) < Cutoff) { :"

v1.0.3

Bugs fixed:

Fixed the annolist issue.

Improvements:

Codes added to avoid using markers selected for variance ratio estimation in the GRM construction.

1.0.2

Bugs fixed:

if LOCO = FALSE, --chrom is

• not required for set-based tests for VCF, BGEN or PLINK input
• not required for single-variant assoc tests for BGEN or PLINK input
• required for single-variant assoc tests for VCF input

if LOCO = TRUE, --chrom is always required

Improvements:

Sample file for bgen input now can either contain one column without header or be in the format of the bgenix (UKBB provided)

v1.0.1

Bugs fixed:
--AlleleOrder for bgen input
Header of the single-variant assoc test output

Improvements:
change PI to M_PI in CCT.cpp
add flag in Makevar for installation on Centos 8

SAIGE-GENE+ implemented

This is the first stable version of SAIGE and SAIGE-GENE+

• Computational efficiency improved for both Step 1 and Step 2
• To obtain a DOI