GLIMPSE

this repo is to store all the WDLs needed to run GLIMPSE.

• following the GLIMPSE tutorial to make these methods https://odelaneau.github.io/GLIMPSE/tutorial.html#run_preliminaries
• docker: https://hub.docker.com/repository/docker/vanallenlab/glimpse

reference files (hg19)

• reference genome: gs://fc-f36b3dc8-85f7-4d7f-bc99-a4610229d66a/broadinstitute/reference/hg19/fasta/Homo_sapiens_assembly19.fasta
• genetic map (used in glimpse_phase): https://ftp.ncbi.nlm.nih.gov/hapmap/recombination/2011-01_phaseII_B37/
• gnomad af (uesd in glimpse_concordance): gs://gnomad-public/release/2.1/vcf/genomes/
• 1000G vcfs: gs://genomics-public-data/ftp-trace.ncbi.nih.gov/1000genomes/ftp/release/20130502/