v2.0.0

What's Changed

• Support of msav file format for reference panels. m3vcf is not supported anymore.
• Add refpanel option to limit the number of allowed allele switches by @seppinho in #132
• Improve and optimize PGS calculation by @lukfor. All scores are merged to a single file for better performance.
• Export of results: Results are not exported for the PGS workflow. Does not change default behaviour of Imputation Workflow.

Full Changelog: v1.8.0...v2.0.0

v2.0.0-beta2

What's Changed

• Add refpanel option to limit allowed allele switches by @seppinho in #132

Full Changelog: v2.0.0-beta1...v2.0.0-beta2

v2.0.0-beta1

Prepare release 2.0.0-beta1

v1.8.0-beta4

Support reference panels in msav format and decay parameter (#128)

* Add new minimac4 binary and adapt execution command

* Add msav reference panels

* Adapt test data to include GT tag

* Fix input data

* Fix input data for hg38 test cases

* Ignore obsolete --myChromosome option

* Update run-tests.yml

* Update run-tests.yml

* Update to new parameter --sites for writing info files

* Add new minR2 parameter to minimac4 and remove R2 pipeline filter

* Add prefix mis_ to all MIS tags in VCF file

* Fix VCF header test case with new prefix

* Update to latest minimac4 binary

* Add min-r2 parameter to command only if minR2 > 0

* Update to pgs-calc version v0.9.10

* Prepare release v1.7.0-rc1

* Update to latest minimac4 (commit 9c653eb)

* Prepare release 1.7.0-rc2

* Update minimac4 to 8498d

* Add HTS tag to m4 format option

* Update minimac4 and rebuild msav files

* Update DefaultPreferenceStore.java

* Fix line number in new test case (from master) due to new M4

* Update to minimac v4.1.0

* Update to minimac v4.1.4

* Add minimac4 decay option

* Prepare release v1.8.0-beta1

* Update imputation engine log to v4.1.4

* Prepare release v1.8.0-beta2

* Update to minimac v4.1.5

* Prepare release v1.8.0-beta3

* Prepare release v1.8.0-beta4 (#126)

Provenance: from installer script
https://github.com/statgen/Minimac4/releases/tag/v4.1.6

---------

Co-authored-by: Andy Boughton <[email protected]>

v1.8.0

What's Changed

• Support reference panels in msav format and decay parameter by @seppinho in #128

Full Changelog: v.1.7.5...v1.8.0

v1.8.0-beta3

• Update to minimac v4.1.5

v1.8.0-beta2

What's Changed

• Update to latest Minimac4 v4.1.4
• Migrate to msav ref panels only
• Update msav-support by @seppinho in #121

v.1.7.5

Prepare release 1.7.5

v1.7.4

What's Changed

• Update genepi maven repository by @lukfor in #114
• Add escape to error messages by @lukfor and @seppinho in #117

Full Changelog: v1.7.3...v1.7.4

v1.7.3

What's Changed

• Remove url-based uploads and check for missing files by @seppinho in #106
• Check for missing files in Input Validation step by @seppinho in #107
• Remove url upload from docs by @lukfor in #105

Full Changelog: v1.7.2...v1.7.3