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konradjk / exac_browser

Browser for ExAC consortium data
http://exac.broadinstitute.org
MIT License
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Subset missing from ftp site for ExAC.r0.3.1 release? #270

Closed kilodalton closed 7 years ago

kilodalton commented 8 years ago

I have tried to send a few emails to the contact email on http://exac.broadinstitute.org/contact but haven't heard back...My apologies if there is a better way (than making an issue/ticket on the repo) to send this request:

The nonpsych data subset is available for the "release0.3" data set but is absent from the "release0.3.1" data set on the FTP site (ftp://ftp.broadinstitute.org/pub/ExAC_release/release0.3.1/subsets/). Could the nonpsych data set be made available for that release (in that subdirectory or somewhere else)?

The release notes mention that the nonpsych data should be on the ftp site for this release:

ftp://ftp.broadinstitute.org/pub/ExAC_release/release0.3.1/README.ftp_structure

"== subsets ===: This directory contains two commonly requested subsets from ExAC release 0.3.1 (60,706 samples) ExAC.r0.3.1.nonTCGA.sites.vep.vcf.gz - Excluding TCGA cohorts (53,105 samples) ExAC.r0.3.1.nonpsych.sites.vcf.gz - Excluding Psychiatric cohorts (45,376 samples)"

Presumably named from the above snippet the files in the subsets dir would be ExAC.r0.3.1.nonpsych.sites.vcf.gz ExAC.r0.3.1.nonpsych.sites.vcf.gz.tbi

Thanks for the help!

kilodalton commented 8 years ago

@konradjk Will the nonpsych subset can be added for the 0.3.1 release? @monkollek indicated that the only difference between 0.3 and 0.3.1 are that additional (convenience) annotations have been added to 0.3.1 and that you would be the one to contact to see if the ExAC.r0.3.1.nonpsych.sites resource would be made available. I realize another release will be coming up in the fall but I just wanted to see if this subset would be added before that.

Thanks for your help!

konradjk commented 7 years ago

This is now in the final 1.0 release, apologies for the delay.

kilodalton commented 7 years ago

@konradjk Thanks for the update! And thanks for the great resource!

alizraksi commented 6 years ago

Can we reopen this issue? It appears that the links are broken to these files, in the 1.0 release. All other links seem to be working. To be more specific, trying to download the following two files in the subsets directory gives me the error: "No such file."

ExAC_nonpsych.r1.sites.vep.vcf.gz ExAC_nonpsych.r1.sites.vep.vcf.gz.tbi