Bug Fixes

• Corrected rna_fq2bam sample code. The --read-files-command zcat, while not a required parameter, is needed for correct operation with compressed FASTQ files.

• Updated the list of supported haplotypecaller options.

• Corrected GATK sample code.

• Fixed an fq2bam bug that occurred when many Ns are present in the fastq files.

General deepvariant performance improvements.