Download all the Reference files

We are using the GATK bundle b37 for most of our reference files.

Following files need to be downloaded (and unzipped):

'1000G_phase1.indels.b37.vcf'
'1000G_phase1.indels.b37.vcf.idx'
'dbsnp_138.b37.vcf'
'dbsnp_138.b37.vcf.idx'
'human_g1k_v37_decoy.dict.gz'
'human_g1k_v37_decoy.fasta.fai.gz'
'human_g1k_v37_decoy.fasta.gz'
'Mills_and_1000G_gold_standard.indels.b37.vcf'
'Mills_and_1000G_gold_standard.indels.b37.vcf.idx'

This file is on our repo so it will be easy ;-)

'centromeres.list'

The last files are made when indexing human_g1k_v37_decoy.fasta with bwa.

'human_g1k_v37_decoy.fasta.pac'
'human_g1k_v37_decoy.fasta.amb'
'human_g1k_v37_decoy.fasta.ann'
'human_g1k_v37_decoy.fasta.bwt'
'human_g1k_v37_decoy.fasta.sa'

You can do that by using your own bwa:

bwa index human_g1k_v37_decoy.fasta

Or using a Docker image containing it:

docker run -v `pwd`:/tmp -w /tmp maxulysse/mapreads:1.0 bwa index human_g1k_v37_decoy.fasta

The rest of the references files are stored in in export.uppmax.uu.se and also on the repository CAW-References using GIT-LFS and :

'1000G_phase3_20130502_SNP_maf0.3.loci'
'b37_cosmic_v74.noCHR.sort.4.1.vcf.idx'
'b37_cosmic_v74.noCHR.sort.4.1.vcf'