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Extremely high (>250GB) memory usage from GenotypeGVCFs w/ moderate-sized GenomicsDb input

33

I am running GATK GenotypeGVCFs, v4.2.6.1. I am trying to call Genotypes on a GenomicsDB workspace with about 500 WGS samples. Note, this is the macaque MMul10 genome, so it...

bbimber

Simplified genotype likelihood calculation (no change in output)

32

@jamesemery Could you review this? I think you may appreciate it. It took several tries, but I was finally able to write a stripped-down version of the code that actually...

davidbenjamin

* DO NOT MERGE * adding base level comparison modes for CompareReferences tool

5

orlicohen

Removed usage of service account from WDLs

2

Removed usage of service account from: GvsAssignIds.wdl GvsImportGenomes.wdl GvsCreateAltAllele.wdl GvsCreateFilterSet.wdl GvsWithdrawSamples.wdl GvsCreateAltAllele.wdl GvsPrepareRangesCallset.wdl GvsExtractCallset.wdl GvsExtractCohortFromSampleNames.wdl GvsUnified.wdl GvsJointVariantCalling.wdl GvsAoUReblockGvcf.wdl GvsBenchmarkExtractTask.wdl GvsRescatterCallsetInterval.wdl

gbggrant

Hello - we're trying to run Funcotator with a custom data source, where that source is a locatableXsv (i.e. simple tab-delimited file with columns for contig, start, and end). I...

bbimber

Investigate GATK error message with docker --network none

1

This error message occurs when removing the network when running GATK in a docker container. GATK tools still run to completion, but the error message is disruptive. ``` $> docker...

GATKSupportTeam

## Bug Report ### Affected tool(s) or class(es) Build ### Affected version(s) - [X] Latest public release version [version?] - [ ] Latest master branch as of [date of test?]...

yurivict

New tools for annotation-based filtering.

9

This is a meta issue to track remaining and future work for the new tools for annotation-based filtering, which will hopefully replace VQSR. Internal developers may want to see further...

samuelklee

We already have a battery of carrot tests that we would like to run to evaluate the HaplotypeCaller. However those tests do not currently cover any of the new use...

jamesemery

- version GATK4.2.6.1 Hi, When I use the following command to genotype a single g vcf file, the output **alt depth**(ref depth is ok) in the FORMAT column are missing....

xiucz