gatk legacy bundles (where to get Mills_and_1000G_gold_standard.indels.hg19.sites.vcf.gz)

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Nick Kinney

• June 24, 2021 16:08

I need the known indels vcf to run gatk BaseRecalibrator. I need hg19 (not the b37) version of the known indels: Mills_and_1000G_gold_standard.indels.hg19.sites.vcf.gz

However this file is no longer available at: ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/hg19/Mills_and_1000G_gold_standard.indels.hg19.sites.vcf.gz

the broad institute documentation says the ftp site was disabled last year (https://gatk.broadinstitute.org/hc/en-us/articles/360035890811) so I checked the gcp bucket using the following command: gsutil ls gs://gatk-legacy-bundles/hg19/

output:

gs://gatk-legacy-bundles/hg19/
gs://gatk-legacy-bundles/hg19/ucsc.hg19.dict
gs://gatk-legacy-bundles/hg19/ucsc.hg19.fasta
gs://gatk-legacy-bundles/hg19/ucsc.hg19.fasta.fai

In other words, I cant find Mills_and_1000G_gold_standard.indels.hg19.sites.vcf.gz in the gatk-legacy-bundles bucket. Does anyone know where this file is now available for download?

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  Sonia Wolf

  • July 13, 2021 12:59

  Hi Nick,

   

  Can't help but am looking for the same thing so would be interested in the answers!

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  Nick Kinney

  • July 13, 2021 15:05

  Sonia Wolf for some reason the ftp site wasn't working for me and all of a sudden worked. Who knows, try 

  wget ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/hg19/Mills_and_1000G_gold_standard.indels.hg19.sites.vcf.gz

  If you get stuck ill sent it to you, regardless, I still dont see all the legacy files in the google bucket.

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  Genevieve Brandt (she/her)

  • July 13, 2021 23:38

  Thanks for the update Nick Kinney! Does this answer all your above questions?

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