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.