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### Instructions * Hi, I am using gatk 4.3.0.0 * found a mutant filtered by "strand bias", please see the following record * found two depth table named "AS_SB_TABLE" and...

gudeqing

GenomicsDBImport sorting issue

11

## Bug Report ### Affected tool(s) or class(es) GenomicsDBImport ### Affected version(s) Latest ### Description Output from GenomicsDBImport is sorting based on alphabetic order: chr 10 ahead of chr 7...

EsperanzaDai

Hello, When using JEXL expressions, is there a good built-in solution for handling both single and multi-allelic sites? A good example is trying to filter on AF, which could be...

bbimber

Added long read walkers from long-running branch.

1

Fixed warnings in long read tools that were pulled in.

jonn-smith

* Add new parameter to set filtered genotypes to no-calls to ExtractCohort * Modified ExtractCohortEngine to optionally set genotypes that are filtered (FT flag set - at the genotype leve)...

gbggrant

Bug fix in flow allele filtering

1

A really tiny bug fix. Apparently allele filtering did not work well in case the allele with high SOR was not the one with the lowest quality.

ilyasoifer

This PR fixes an error in the cost calculation in that we were not handling pre-emption. That is, a shard could get preempted and thus we'd have multiple cost measurements...

gbggrant

Test out the preview version of the next GKL (DO NOT MERGE)

16

Test out the preview version of the GKL, containing the new native PDHMM. The jar was build using Java 1.8 and contains AVX optimized binaries for Linux hosts and not...

droazen

Prevent users enabling annotations with mismatching data type (flow etc)

7

Here is an user trying to enable flow based annotations for non-flow data. https://gatk.broadinstitute.org/hc/en-us/community/posts/24596063911963-Error-while-running-Mutect2-java-lang-IllegalArgumentException-the-index-points-past-the-last-element-of-the-collection-or-array-334-333 What could be done to prevent this? Possible ideas - Check data and disable nonmatching annotations...

gokalpcelik

Allow for GT to be a nocall if GQ and PL[0] are zero instead of homref in GenomicsDB

8

As a result of #8715, GenomicsDB supports GT to be nocall when GQ and PL[0] are zeroes. See https://github.com/GenomicsDB/GenomicsDB/pull/332.

nalinigans