| Deposited data |
|
| GWAS summary statistics |
This study |
https://canpath.ca/ |
| Melanocyte genotype data |
(Zhang et al., 2018) |
dbGaP phs001500.v1.p1 |
| RNA-seq expression data |
(Zhang et al., 2018) |
dbGaP phs001500.v1.p1 |
| meQTL association results |
(Zhang et al., 2021) |
dbGaP phs001500.v1.p1 |
|
| Software and algorithms |
|
| QC Perl script |
McCarthy Group Tools |
https://www.well.ox.ac.uk/∼wrayner/tools/ |
| PLINK 1.9 |
PLINK Working Group (Purcell et al., 2007; Chang et al., 2015) |
https://www.cog-genomics.org/plink/ |
| Sanger Imputation Server |
Wellcome Sanger Institute (McCarthy et al., 2016) |
https://www.sanger.ac.uk/tool/sanger-imputation-service/ |
| PLINK 2.0 |
PLINK Working Group (Purcell et al., 2007; Chang et al., 2015) |
https://www.cog-genomics.org/plink/2.0/ |
| R version 3.5.1 |
R Core Team (R Core Team, 2019) |
https://www.r-project.org/ |
| GCTA version 1.26.0 |
(Yang et al., 2011, 2012, 2014) |
https://yanglab.westlake.edu.cn/software/gcta/#Overview |
| METASOFT version 2.0.1 |
(Han and Eskin, 2011) |
http://genetics.cs.ucla.edu/meta/ |
| LocusZoom |
(Pruim et al., 2011) |
http://locuszoom.org/ |
| SNPNexus |
(Ullah, Lemoine and Chelala, 2012; Ullah et al., 2018) |
https://www.snp-nexus.org/v4/ |
| FINEMAP version 1.4 |
(Benner et al., 2016) |
http://www.christianbenner.com/ |
| LDStore version 2.0 |
(Benner et al., 2016) |
http://www.christianbenner.com/# |
| HaploReg version 4 |
(Ward and Kellis, 2012, 2016) |
https://pubs.broadinstitute.org/mammals/haploreg/haploreg.php |
| CASSI |
(Howey, 2017) |
https://www.staff.ncl.ac.uk/richard.howey/cassi/using.html |
| HyPrColoc |
(Foley et al., 2021) |
https://github.com/jrs95/hyprcoloc |
| FUSION |
(Gusev et al., 2016) |
http://gusevlab.org/projects/fusion/ |
