https://42basepairs.com/browse/gs/deepvariant/models/DeepVariant # models are included in the docker image, no download needed in most cases
https://github.com/broadinstitute/tandem-repeat-catalog/releases # needed for trgt
# kraken2 database download: https://benlangmead.github.io/aws-indexes/k2
# small variants: wget ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/VCF/00-All.vcf.gz # this is dbsnp, hg38
# annotsv data: install annotsv as described in the quickstart page on github`s readme
# sansa: hgsvc data from official webpage, gnomad also an option but much bigger dataset
# reference genome: ucsc, ensembl or from illuminas reference genome bucket (igenome) or from hgsvcs ftp page, there you can also find hg38 without alt chroms
# vep cache currently with awscli: aws s3 --no-sign-request --region eu-west-1 sync s3://annotation-cache/vep_cache/115_GRCh38/ .