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

Question

[nkinney06]

I need the known indels vcf to run gatk BaseRecalibrator. So 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://[e-mail]/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?

[GenoMax]

The files are available in this bucket.

[nkinney06]

Thanks but those are all hg38 not hg19. I know about liftover tools but the file I need should still be available

[GenoMax]

Your best bet may be to ask GATK support. hg19 version does not seem to be readily available via a search.

[Edmond]

These files are for hg38, not hg19. Do you know were are the files for hg19 ?

[GenoMax]

Please ask GATK support via their forum and then come back to provide that information here for future visitors.

Answer 1

[ning]

You can find the legacy bundle at their ftp site, but you have to be logged in as gsapubftp-anonymous (logging in as anonymous will not show the bundle).

ShujiaHuang on GitHub provides some wget commands to retrieve those files:

[Ishak]

thanks soooooo much