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@allgenesconsidered
Last active September 26, 2023 08:04
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Pulling more reference files from the GATK servers
#!/bin/bash
cd /data/home/molvera/res
wget -c ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/hg38/1000G_phase1.snps.high_confidence.hg38.vcf.gz
wget -c ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/hg38/1000G_phase1.snps.high_confidence.hg38.vcf.gz.tbi
wget -c ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/hg38/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz
wget -c ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/hg38/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi
wget -c ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/hg38/hapmap_3.3.hg38.vcf.gz
wget -c ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/hg38/hapmap_3.3.hg38.vcf.gz.tbi
wget -c ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/hg38/dbsnp_146.hg38.vcf.gz
wget -c ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/hg38/dbsnp_146.hg38.vcf.gz.tbi
wget -c ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/hg38/1000G_omni2.5.hg38.vcf.gz
wget -c ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/hg38/1000G_omni2.5.hg38.vcf.gz.tbi
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