Version 1.3.17

This version modified SampleSpecificGenotypeFilter to add support for --set-filtered-genotypes-to-no-call

Version 1.3.16

This release adds a new tool to summarize genotypes by quality.

What's Changed

• Add SummarizeGenotypeQuality tool by @bbimber in #188

Full Changelog: 1.3.15...1.3.16

Version 1.3.15

This version adds a new tool that takes a VCF and a set of intervals, and will output only variants starting in those intervals.

What's Changed

• Add tool to OutputVariantsStartingInIntervals by @bbimber in #187

Full Changelog: 1.3.14...1.3.15

Version 1.3.14

What's Changed

• Bump docker/build-push-action from 3.0.0 to 3.1.0 by @dependabot in #184
• Bump docker/build-push-action from 3.1.0 to 3.1.1 by @dependabot in #185
• Tool for sample-specific Genotype JEXL filtering by @bbimber in #186

Full Changelog: 1.3.13...1.3.14

Version 1.3.13

This version updates two tools:

• VariantConcordanceScore now uses a weighted method based on reference allele frequencies
• MergeVariantSites was refactored to use MultiVariantWalkerGroupedByStart for faster performance

Version 1.3.12

This adds a new mGAP-specific tool that takes a VCF and annotates it based on whether those sites are present in a reference VCF

Version 1.3.11

This fixes a bug in the date format used in the VariantQC report

Version 1.3.10

Update to GATK 4.2.4.1, which includes more log4j patches

Version 1.3.9

Update to GATK 4.2.4.

Version 1.3.8

Add flag in IntegrationSiteMapper to allow inclusion of reverse reads.