gatk

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Added a check for whether files can be created and executed within the configured tmp-dir

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Adds a couple warnings in case the user can write to the configured tmp-dir but can't set the files as executable or execute them, with the assumption in the latter...

KevinCLydon

Engine read caching.

2

Allow tools to opt-in for read caching (enabled in this PR for CNNScoreVariants and FilterAlignmentArtifacts) when issuing forward-only queries such as those used to query a ReadsContext for all reads...

cmnbroad

GermlineCNVCaller - python exited with 2

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Hello, I'm testing gatk4.3 against 3 WES samples. For less time comsuption, I scattered the bed file into 45 small interval list. But an error prompted out in the GermlineCNVCaller...

lovelycatZ

[log](https://freebsd.org/~yuri/gatk-4.6.0.0-tests-5.log) Examples of test failures from the above log: ``` Running Test: Test method testRequirePythonEnvironment(org.broadinstitute.hellbender.utils.python.StreamingPythonExecutorIntegrationTest) Gradle suite > Gradle test > org.broadinstitute.hellbender.utils.python.StreamingPythonExecutorIntegrationTest > testRequirePythonEnvironment FAILED java.lang.NullPointerException: Cannot invoke "Object.getClass()" because...

yurivict

Some print messages like this: ``` Gradle suite > Gradle test > org.broadinstitute.hellbender.utils.smithwaterman.SmithWatermanIntelAlignerUnitTest > testSubstringMatchLong[0](359, 7M, SOFTCLIP) STANDARD_ERROR 03:09:09.419 WARN NativeLibraryLoader - Unable to load libgkl_utils.so from native/libgkl_utils.so (/tmp/libgkl_utils7398935100372553580.so: Shared...

yurivict

The testsuite seems to merge outputs of all tests into the same output stream, which makes it difficult to read. Please consider improving testsuite output to show only one or...

yurivict

Adds an option to SVCluster to disable output sorting/indexing. Since sorting requires holding an indeterminate number of records in memory, it can substantially inflate memory usage. Analagous to #8623.

mwalker174

CreateSomaticPanelOfNormals: multiallelic sites wrongly added to PON despite --min-sample-count set to total input samples

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## Bug Report ### Affected tool(s) or class(es) CreateSomaticPanelOfNormals, argument --min-sample-count ### Affected version(s) - 4.4.0.0 ### Description I followed all the guidelines listed [here](https://gatk.broadinstitute.org/hc/en-us/articles/13832769396635-CreateSomaticPanelOfNormals-BETA) to build a PON. This...

juliawiggeshoff

gatk Funcotator error

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Hi, when I run gatk Funcotator, A USER ERROR has occurred ``` Using GATK jar /export/.conda/envs/wes/share/gatk4-4.0.5.1-0/gatk-package-4.0.5.1-local.jar Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /export/bioinfo-team/home/liuhw/.conda/envs/wes/share/gatk4-4.0.5.1-0/gatk-package-4.0.5.1-local.jar Funcotator --data-sources-path /export2/liuhw/software/gatk_Funcotator/funcotator_dataSources.v1.8.hg38.20230908s/ -V /export2/liuhw/wes_test//Mutect2_filter/K001137N_somatic_filtered.vcf.gz -R...

l-magnificence

Hello, I'm using gatk 4.2.2.0 with PathSeqPipelineSpark but I'm having some problems. For some samples I have the generation of the outuput.bam file while for others no. gatk --java-options "-Xmx750G"...

martitroiani