## Align reads using Parabricks fq2bam, which includes BWA mem, BQSR, markduplicates, and sorting / indexing of the bam
## Assumes pbrun has been copied to /usr/local/bin or some other acessible path
pbrun fq2bam \
  --in-fq HG002.hiseqx.pcr-free.30x.R1.fastq.gz HG002.hiseqx.pcr-free.30x.R2.fastq.gz \
  --ref GCA_000001405.15_GRCh38_no_alt_analysis_set.fna \
  --known-sites dbsnp_146.hg38.vcf.gzz \
  --out-bam HG002.hiseqx.pcr-free.30x.pb.bam \
  --out-recal-file HG002.hiseqx.pcr-free.30x.pb.recal.txt \
  --num-gpu 4