v1.1.4

• Hotfix for handling * alleles (signifying overlapping deletion) from GATK and GATK-based callers. The representation can still be improved.
• Set default gatk.unifier_config.max_alleles_per_site = 70
• Internal optimizations #144, #147 (@xunjieli)

v1.1.3

set weCall.unifier_config.max_alleles_per_site = 70

Experimental Strelka2 support

With --config Strelka2 GLnexus can merge Strelka2 gVCFs into pVCF. This is highly experimental right now (first attempt that produced well-formed output).

Bump a few dependency revisions

Fix two DeepVariant corner cases

• Don't call 0/0 from reference bands whose GT is not 0/0
• Fix obscure code path triggered by cluster of non-normalized gVCF alleles: monoallelic indel which some discovered allele didn't originally overlap, then got realigned and unified

The DeepVariant configuration remains experimental!

xAtlas calibration, QC squeezing

• Major improvements to xAtlas configuration including calibrated AQ filtering and genotype revision in the xAtlas configuration preset. There is also an xAtlas_unfiltered preset with those features disabled. (#138)
• Optional "squeezing" of output pVCF reduces pVCF size and runtime by reporting fewer QC details for most reference-identical genotypes. (#136)
  • Currently opt-in with --squeeze, -S but planned to become the default
  • Further compression is possible by piping into spVCF for squeezing and/or sparse encoding.
• Minor:
  • pVCF DP is filled in with gVCF MIN_DP instead of DP when both are present
  • Accept rare HaplotypeCaller variant records with no AD or DP fields (considers all depths zero)
  • Automatically test Getting Started examples

Fix performance regression

Memory and thread budget parameters introduced in #134 were not taking the desired defaults when not provided on the command-line.

v1.0.1

• Pre-compiled executable has wider compatibility (back to Ubuntu 14.04 and Ivy Bridge CPUs)
• More-reliable warning message if jemalloc is not in use

v1.0.0

GLnexus is v1.0.0! 🍾

This open-source version is now under Apache License 2.0.

test_travis_release

travis: deploy tagged revisions of glnexus_cli to GitHub releases