Generate an HG19 Reference

If you do not have a FASTA reference, you can get the hg19 FASTA files from UCSC and concatenate them into a single hg19.fa file as follows:

mkdir /staging/hg19fa
cd /staging/hg19fa
wget hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/chromFa.tar.gz
tar -zxvf chromFa.tar.gz
cat chr*.fa > hg19.fa

Generate the DRAGEN hash table reference using the following commands.

mkdir /staging/hg19/
dragen --ht-reference /staging/hg19fa/hg19.fa \
    --output-directory /staging/hg19/ --build-hash-table true \
    --ht-alt-liftover /opt/edico/liftover/hg19_alt_liftover.sam