v1.3.6

What's Changed

• Update README.md by @cwarlysolsberg in #212
• Update ancestry.py by @cwarlysolsberg in #210
• Update qc.py by @cwarlysolsberg in #209
• Update genotools_function_guide.md by @cwarlysolsberg in #208
• add neural admixture + relabel problematic EUR samples by @mkoretsky1 in #214
• clean up common_snps later in the pipeline by @mkoretsky1 in #216
• keep ref_common_snps around until the end of ancestry as well by @mkoretsky1 in #217
• id to csv not chr by @mkoretsky1 in #218
• plink2 exec fix by @mkoretsky1 in #219
• add dir name to path by @mkoretsky1 in #220
• add logging to neural-admixture commands to get a better sense of the… by @mkoretsky1 in #221
• add ref snps to exclude in haplotype prune method by @dvitale199 in #222
• remove get_eur_admixed commands from pipeline by @mkoretsky1 in #223
• remove cloud predictions and neural-admixture from ancestry by @mkoretsky1 in #224
• LD flag fix by @mkoretsky1 in #225
• fix nargs by @mkoretsky1 in #226
• fixing ld flag by @mkoretsky1 in #227
• roll back LD pruning to test API errors by @mkoretsky1 in #228
• drop 0 SD SNPs when fitting PCs by @mkoretsky1 in #229
• Model out by @dvitale199 in #230
• add headers to requests for KING download fix by @mkoretsky1 in #231

New Contributors

• @cwarlysolsberg made their first contribution in #212

Full Changelog: v1.3.5...v1.3.6

v1.3.5

What's Changed

• update containerized model to match API by @mkoretsky1 in #204
• Sexcheck by @dvitale199 in #206

Full Changelog: v1.3.4...v1.3.5

v1.3.4

Full Changelog: v1.3.3...v1.3.4

v1.3.3

What's Changed

• het prune before related prune in main pipeline by @mkoretsky1 in #203
• copy files when no related pruning occurs by @mkoretsky1 in #205

Full Changelog: v1.3.2...v1.3.3

v1.3.2

What's Changed

• Update README.md by @dvitale199 in #201

Full Changelog: v1.3.1...v1.3.2

v1.3.1

What's Changed

• Update README.md by @dvitale199 in #197
• Update README.md by @dvitale199 in #198
• Update README.md by @dvitale199 in #199

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

v1.3.0

What's Changed

• Update qc.py by @dvitale199 in #187
• het typo by @sammyhong23 in #188
• Update documentation by @nvk23 in #189
• error catching and tmpdir pipeline fixes by @mkoretsky1 in #190
• move process complete for HWE so its not always True by @mkoretsky1 in #191
• AMR het prune update by @mkoretsky1 in #192
• ancestry-only tmpdir bug fix by @mkoretsky1 in #193
• all samp/var QC'd bug fix by @mkoretsky1 in #194
• fix assoc pipeline error by @mkoretsky1 in #195
• adding option to maf prune during lambda calculation by @mkoretsky1 in #196

Full Changelog: v1.2.4...v1.3.0

v1.2.4

What's Changed

• check for abspath for concat_logs for relative path execution by @dvitale199 in #186

Full Changelog: v1.2.3...v1.2.4

v1.2.3

What's Changed

• Update README.md by @dvitale199 in #177
• separate ancestry from execute_pipeline by @mkoretsky1 in #179
• Update README.md by @dvitale199 in #181
• Update cli_args.md by @dvitale199 in #182
• Related by @dvitale199 in #184
• updated het to +/-0.15 by @dvitale199 in #185

Full Changelog: v1.2.2...v1.2.3

v1.2.2

Full Changelog: v1.2.1...v1.2.2