v1.4.1

Start Here: tutorial

• Recalibrate joint-called GQ values for DeepVariant inputs, reducing excessive downward-biased GQ for 1/1 genotypes of rare alleles in large cohorts
• Genotyper will now never revise 1/1 calls to 0/0
• Compatible with gvcf_norm-preprocessed inputs
• Update dependency versions

glnexus_cli docker image: ghcr.io/dnanexus-rnd/glnexus:v1.4.1

v1.3.1

Start Here: tutorial

• Add genotyper_config::top_two_half_calls option; preserves more diploid calls in certain complex situations (by hiding the complexity)
• Clarify several error messages
• Update dependency versions

glnexus_cli docker image: quay.io/mlin/glnexus:v1.3.1

v1.3.0

This version is retracted -- the executables and Docker image were inadvertently built in a non-portable way

glnexus_cli docker image: quay.io/mlin/glnexus:v1.3.0

v1.2.7

Start Here: tutorial

• Adds DeepVariant_unfiltered config preset (@tedyun)

glnexus_cli docker image: quay.io/mlin/glnexus:v1.2.7

v1.2.6

• Fix sporadic omission of allele IDs in --debug mode (samtools/htslib#1030)
• Update dxapplet to Ubuntu 16.04 image

v1.2.5

• Adds weCall_unfiltered configuration preset
• RocksDB v6.6.4

glnexus_cli docker image: quay.io/mlin/glnexus:v1.2.5

v1.2.4

Start Here: tutorial

• glnexus_cli performance improvements:
  • First pass over the gVCF data, to discover candidate alleles, begins while RocksDB is still reorganizing (compacting) its on-disk storage, improving system utilization and reducing peak memory usage (due to smaller caches used while compactions are running) (#199)
  • Parallelize the allele unifier algorithm (by contig) (#148)
• glnexus_cli --dir /SOME/PATH overrides default $(pwd)/GLnexus.DB/ scratch directory (#142)
• Define AC & AN INFO fields in output pVCF header; GLnexus itself doesn't generate these fields, but they may be added by bcftools post-processing steps in which case it's proper to have them defined in the header (and not harmful otherwise)
• Fix a minor case of non-deterministic output (#176)
• Bump dependency revisions

glnexus_cli docker image: quay.io/mlin/glnexus:v1.2.4

v1.2.3

DeepVariant configuration fine-tuning:

• Set unifier_config::max_alleles_per_site=32 to prevent excessive PL blowup (#201 @xunjieli).
  • Alleles exceeding this limit are "kicked out" into monoallelic rows.
• Set genotyper_config::allow_partial_data=true so that non-called reference bands don't cause non-calling of nearby variants
• Fixes several minor bugs in unifier & genotyper causing (rare) copy number discrepancies between gVCF & pVCF

glnexus_cli docker image: quay.io/mlin/glnexus:v1.2.3

v1.2.2

Set genotyper_config::more_PL and genotyper_config::trim_uncalled_alleles to true in the DeepVariant configuration presets (#196 @cmclean)

glnexus_cli docker image: quay.io/mlin/glnexus:v1.2.2

v1.2.1

Improved handling of DeepVariant non-called gVCF records

Compared to other callers, DeepVariant generates more non-called (GT=./.) gVCF records to represent uncertainty in poorly-covered or ambiguous sites; including both reference bands and variant records. Earlier versions of GLnexus omitted all QC values in the pVCF entries corresponding to such records. This patch preserves the QC values and introduces a new "Reason for No Call" code, I for Input non-called, to indicate the site or reference band was non-called in the gVCF input.

glnexus_cli docker image: quay.io/mlin/glnexus:v1.2.1