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.

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