Reference Resources

Include name, location on server, link to source and when downloaded/created

Summary

Resource	Version	Created/Downloaded
1000 Genomes Project	Phase3	September 2014/March 2017
Human Reference Sequence	GRCh37 (build 37/hg19)	tbc
dbSNP	137	tbc
GATK Resource Bundle	b.37	tbc
1KGP Impute Panel	Phase3	October 2014

Hosted shiny apps

Name	URL
Merriman GTEx eQTL browser	http://biochemcompute.otago.ac.nz:3838/mik-apps/QTLBrowser/

Web Resources

Name	Genome Build	Website
ensembl genome browser	GRCh37	http://grch37.ensembl.org/index.html
ensembl genome browser	GRCh38	http://ensembl.org/index.html
ensembl ftp		ftp://ftp.ensembl.org/pub/
UCSC genome browser	GRCh38	https://genome.ucsc.edu/index.html
UK10K genome browser	GRCh37	http://www.uk10k.org/dalliance.html
dbSNP	GRCh37/38	http://www.ncbi.nlm.nih.gov/projects/SNP/index.html
LocusZoom		http://locuszoom.sph.umich.edu/locuszoom/
eQTL browser		http://www.ncbi.nlm.nih.gov/projects/gap/eqtl/index.cgi
GTEx Portal		http://www.gtexportal.org/home/
Disease Variant Store		https://rvs.u.hpc.mssm.edu/divas/
DAVID		https://david.ncifcrf.gov/home.jsp
Exome Variant Server		http://evs.gs.washington.edu/EVS/
1000 Genomes Project	GRCh37	http://1000genomes.org/
1000 Genomes Project ftp		http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/
Sanger Impute Server		https://imputation.sanger.ac.uk/
HapMap Project	GRCh36	http://hapmap.ncbi.nlm.nih.gov/
SHEsis		http://analysis.bio-x.cn/myAnalysis.php
SNAP proxy		https://www.broadinstitute.org/mpg/snap/ldsearch.php
Strand files		http://www.well.ox.ac.uk/~wrayner/strand/
Genome Reference Consortium		http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/
NCBI Genome ReMapper		http://www.ncbi.nlm.nih.gov/genome/tools/remap#
GWAS Catalog		www.ebi.ac.uk/gwas/
GWAS Central		www.gwascentral.org
UK Biobank		http://biobank.ctsu.ox.ac.uk/crystal/
UK Biobank ICD explorer		http://risteys.broadinstitute.org

1000 Genomes Project

Phase 3 release from September 2014 location: /Volumes/archive/merrimanlab/reference_files/VCF/1000Genomes_vcf_files/Phase3_Sept2014

Phase 3 release from March 2017 location: /Volumes/archive/merrimanlab/reference_files/VCF/1000Genomes_vcf_files/Phase3_March2017

Both are in GRCh37 coordinates.

Impute2 reference panel

GRCh37 coordinates

https://mathgen.stats.ox.ac.uk/impute/1000GP_Phase3.html

Human Reference Sequence

GRCh37 Decoy reference

Downloaded 5 Aug 2014

url: ftp://ftp.1000genomes.ebi.ac.uk:21/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz

Location: /Volumes/archive/merrimanlab/reference_files/FASTA/hs37d5/hsd37d5.fa

dbSNP

dbSNP 151 is available in both GRCh37 and GRCh38 genome builds as a vcf at /Volumes/archive/merrimanlab/reference_files/VCF/dbSNP_reference/dbsnp151/

GRCh37 is from 2018-04-23

GRCh38/Hg38 is from 2018-04-18

GATK Resource Bundle

Crucial resource for running the GATK.

More information: http://gatkforums.broadinstitute.org/discussion/1213/whats-in-the-resource-bundle-and-how-can-i-get-it

Ancestral allele

Downloaded 6 Aug 2014

url: ftp://ftp.ensembl.org/pub/release-66/fasta/ancestral_alleles/homo_sapiens_ancestor_GRCh37_e66.tar.bz

/Volumes/archive/merrimanlab/reference_files/Ancestral_Alleles/homo_sapiens_ancestor_GRCh37_e65/

Reference Resources