gatk legacy bundles (where to get Mills_and_1000G_gold_standard.indels.hg19.sites.vcf.gz)
0
0
Entering edit mode
5 months ago
nkinney06 ▴ 90

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://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?

indels gatk • 997 views
ADD COMMENT
0
Entering edit mode

The files are available in this bucket.

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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

ADD REPLY

Login before adding your answer.

Traffic: 2659 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6