Bug Fixes

minimap2: Fixed a memory leak that was exposed by using a different matching score in the updated preset values.

minimap2: Fixed a bug that caused some incorrect SA tag values.

minimap2: Fixed a crash caused by pthread_setaffinity_np.

fq2bam (BWA-MEM + GATK): Fixed a crash when passing --bwa-options="-C" with no comments in the input fastq file(s).

mutectcaller: Fixed an invalid GPU memory access in force calling mode (--mutect-alleles).

mutectcaller: Fixed additional records in output VCF file when passing --pon.

somatic (Somatic Variant Caller): Fixed a read group ID conflict error in tumor-normal mode when --tumor-read-group-id-prefix was not passed from the user.

haplotypecaller: Fixed an out-of-order issue in the output BAM when passing --htvc-bam-output.

deepvariant: Fixed a bug where certain kernels from multiple pipelines (streams) were launched on the default stream.