CoMorMent-Containers-v1.3.7

This is 7th minor/bugfix release of the CoMorMent-Containers project since v1.3.0 release
Confer also the CHANGELOG for an overview of changes since the v1.3.0 release

What's Changed

• LDpred2/createBackingFile.R: process .bgen files by @espenhgn in #200

Full Changelog: v1.3.0...v1.3.7

CoMorMent-Containers-v1.3.6

This is 6th minor/bugfix release of the CoMorMent-Containers project since v1.3.0 release
Confer also the CHANGELOG for an overview of changes since the v1.3.0 release

What's Changed

• LDpred2.R: if --merge-by-rsid is used, ignore --col-bp <arg> by @espenhgn in #193

Full Changelog: v1.3.0...v1.3.6

CoMorMent-Containers-v1.3.5

This is 5th bugfix release of the CoMorMent-Containers project since v1.3.0 release
Confer also the CHANGELOG for an overview of changes since the v1.3.0 release

What's Changed

• Info on ldpred2.R --help functionality by @espenhgn in #192

Full Changelog: v1.3.0...v1.3.5

CoMorMent-Containers-v1.3.4

This is 4th bugfix release of the CoMorMent-Containers project since v1.3.0 release
Confer also the CHANGELOG for an overview of changes since the v1.3.0 release

What's Changed

• Fix #187 by @ofrei in #188

Full Changelog: v1.3.0...v1.3.4

CoMorMent-Containers-v1.3.3

This is 3rd bugfix release of the CoMorMent-Containers project since v1.3.0 release
Confer also the CHANGELOG for an overview of changes since the v1.3.0 release

What's Changed

• Fix LDpred2 error with uppercase chromosome column header by @espenhgn in #180
• Documentation fixes by @espenhgn in #182
• LDpred2: Removed counting of missing genotypes by @deepchocolate in #183
• Fix #174 - sync releases to TSD by @ofrei in #184

Full Changelog: v1.3.0...v1.3.3

CoMorMent-Containers-v1.3.2

This is 2nd bugfix release of the CoMorMent-Containers project since v1.3.0 release
Confer also the CHANGELOG for an overview of changes since the v1.3.0 release

What's Changed

• Fix LDpred2 error with uppercase chromosome column header by @espenhgn in #180
• Documentation fixes by @espenhgn in #182

Full Changelog: v1.3.0...v1.3.2

CoMorMent-Containers-v1.3.1

This is 1st bugfix release of the CoMorMent-Containers project since v1.3.0 release
Confer also the CHANGELOG for an overview of changes since the v1.3.0 release

What's Changed

• Fix LDpred2 error with uppercase chromosome column header by @espenhgn in #180

Full Changelog: v1.3.0...v1.3.1

CoMorMent-Containers-v1.3.0

This is the 3rd maintenance/feature release of the CoMorMent-Containers project.
Confer also the CHANGELOG for an overview of changes since the v1.2 release

What's Changed

• LDPred2: Effective sample size, cores used, hyperparameters by @deepchocolate in #173
• prep 1.3.0 release by @espenhgn in #176

Full Changelog: v1.2...v1.3.0

CoMorMent-Containers-v1.2

CoMorMent-Containers-v1.2

This is the 2nd maintenance/feature release of the CoMorMent-Containers project.
Confer also the CHANGELOG for an overview of changes since the v1.1 release

What's Changed

• LDpred2 fixes by @deepchocolate in #94
• LDpred2.R uses external ld matrix (partial fix for #108) by @ofrei in #109
• add citation.cff and badges by @espenhgn in #113
• set appropriate number of CPU cores by @espenhgn in #115
• Remove reference to ldsc.sif (moved) by @espenhgn in #114
• QQ plots w. confidence bands by @ttfiliz in #118
• unit tests for gwas.py by @ttfiliz in #119
• --variance-standardize for columns without variation by @ttfiliz in #121
• Deepchocolate/ldpred2 updates fixes by @espenhgn in #122
• Allow custom name for IID columns by @ofrei in #123
• update config for flake8 linter by @espenhgn in #126
• Reformat gwas.py and combine_figures.py by @ofrei in #128
• removed redundant --sumstats-sep arg by @espenhgn in #129
• LD-estimation for LDpred2 using bigSNPR by @deepchocolate in #117
• change home to temporary folder in test_gwas_king by @ttfiliz in #136
• Change repo for R packages in r.sif by @espenhgn in #132
• some minor fixes to LDpred2 imputation by @espenhgn in #139
• LDpred2 imputation by @deepchocolate in #131
• removed redundant LDpred2 example by @espenhgn in #141
• Remove --file-pheno, --col-pheno and --col-pheno-from-fam args in ldpred2.R scripts by @espenhgn in #142
• LDpred2: Testing produced scores against tutorial results by @deepchocolate in #146
• Sumstats: Add column and position by @deepchocolate in #143
• LDpred2: Append score to existing output file by @deepchocolate in #150
• fixed print statements by @espenhgn in #156
• Make complementSumstats.R write file output by default by @espenhgn in #159
• clarify --geno-file-rds arg by @espenhgn in #161
• fixed bad parsing of args by @espenhgn in #164
• bumped version to reflect current state by @espenhgn in #166
• Restructured file and folder layout by @espenhgn in #167
• Add RELEASES.md file by @espenhgn in #170
• Prep release v1.2 by @espenhgn in #172

New Contributors

• @ttfiliz made their first contribution in #118

Full Changelog: v1.1...v1.2

CoMorMent-Containers-v1.1

CoMorMent-Containers-v1.1

This is the first maintenance/feature release of the CoMorMent-Containers project.
Confer also the CHANGELOG for an overview of changes since the initial v1.0.0 release

What's Changed

• Fixes incorrect --vcfField format by @rzetterberg in #24
• Resolves #34 by @rzetterberg in #35
• Split out mixer by @ofrei in #53
• Add issue/PR templates by @espenhgn in #48
• migrating files from GH/comorment/gwas@47a23f0 by @espenhgn in #51
• Remove libquadmath0 from builds by @espenhgn in #60
• Use Mambaforge for python3.sif builds by @espenhgn in #63
• Revise Minimac4/bgenix installation in gwas.sif by @espenhgn in #64
• Bump base image to Ubuntu:20.04 by @espenhgn in #65
• Pin software versions by @espenhgn in #66
• Basic test suite by @espenhgn in #67
• Add Shapeit4 (and dependency HTSlib) to gwas.sif by @espenhgn in #71
• GH actions (docker&python lint, greetings, stale) by @espenhgn in #72
• add FaST-LMM v0.6.3 to python3.sif by @ofrei in #74
• Remove broken links to MiXeR usage scenarios by @ofrei in #82
• Add tests for metal, qctool ingwas.sif. by @espenhgn in #84
• LD score regression moved to separate github repo by @ofrei in #86
• Strip container builds of source files etc. by @espenhgn in #79
• Remove ldsc.sif file by @ofrei in #87
• clean up install of htslib, bcftools, shapeit4 by @espenhgn in #89
• r.sif: add R bigsnpr and related tools for LDpred2 analysis by @espenhgn in #91
• Add autogeneration of documentation using Sphinx by @espenhgn in #88
• updated changelog for future v1.1 by @espenhgn in #97
• Split out matlab by @ofrei in #98
• Move MAGMA, LAVA, ldblock to comorment/magma repo by @ofrei in #100
• Move out enigma-cnv.sif , ipsychcnv.sif, tryggve_query.sif by @ofrei in #101
• some changelog/readme updates for v1.1 by @espenhgn in #99

New Contributors

• @ofrei made their first contribution in #53

Full Changelog: v1.0.0...v1.1