4.2.0-1 Release Notes
Several packages have been updated to GATK 4.3. Support for read lengths of up to 500 base pairs has been added to haplotypecaller and mutectcaller.
Several performance improvements.
A number of bugs have been fixed.
Added markdup, a tool to locate and tag duplicate reads in a BAM or SAM file, where duplicate reads are defined as originating from a single fragment of DNA.
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Major performance improvements.
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Supports read lengths of up to 500 base pairs.
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Updated to GATK 4.3.
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Supports read lengths of up to 500 base pairs.
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Adds support for the
--htvc-bam-outputoption. -
--batchis deprecated.
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Updated to GATK 4.3.
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Supports read lengths of up to 500 base pairs.
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Adds support for the
--run-partitionoption.
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Updated to GATK 4.3.
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Clarified error messages.
Improvements spanning multiple tools
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Added more error checking when writing BAM files using
--gpuwrite. -
Improved performance for BWA alignment, particularly for reads > 250 bases in length.
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Added GPUDirect Storage (GDS) support for fq2bam (BWA-MEM + GATK) and associated pipelines.
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Added a low memory mode for
--gpuwrite(affects sorting).
deepvariant Could only handle 32 alt alleles per candidate; can now handle up to 64.
bamsort Bamsort could fail for certain coordinate sorts.
For further information see the Parabricks datasheet.