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exomiser / Exomiser

A Tool to Annotate and Prioritize Exome Variants
https://exomiser.readthedocs.io
GNU Affero General Public License v3.0
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Retrospective study #287

Open laucc opened 6 years ago

laucc commented 6 years ago

Hello,

I am attempting to do a retrospective study on how well Exomiser might have helped in our gene discovery process.

We are hoping to run searches for phenotypic matches against archived databases at certain time points: for instance what's available in 2015 and before, or what's available in 2010 and before.

My question: is that doable with Exomiser, or if we run an older version of Exomiser, are we searching against archived databases that was made prior to the release of newer version?

Thank you for your help and suggestions.

Chris

julesjacobsen commented 6 years ago

Hi Chris

I'm not completely clear what you're trying to achieve. Exomiser versions come with their own versioned databases e.g. version 7 ran on a database produced at that time. The software has obviously changed over time too but it would give you an honest snapshot of how things were then.

The exomiser databases are embedded so come as versioned snapshots, but the earliest version available is version 6 from Feb 2015.

laucc commented 6 years ago

Hi Jules,

Thank you for your email, your answers are very helpful, we are attempting to do exactly what you stated: to have an honest snapshot of how things were, particularly for the cases that we were diagnosing at the NIH UDP. For a good portion of our cases, the diagnosis journey take years, and we are attempting to retrospectively document the accumulation of evidences through the years for these cases.

What is the best way to run the older versions? Is there a site where we can download them (the older version) that you can point us to? Or can we utilize alternate database/HPO-term dictionary using your current version? Please advise.

Thanks, Chris

Christopher Lau, PhD, FACMG NIH Undiagnosed Diseases Program, Building 50, Room 5523 MSC 8004 50 South Drive Bethesda, MD 20892-8004 (o) 301 827 4433 (c) 646 300 2308

From: Jules Jacobsen notifications@github.com Reply-To: exomiser/Exomiser reply@reply.github.com Date: Wednesday, October 17, 2018 at 10:06 AM To: exomiser/Exomiser Exomiser@noreply.github.com Cc: "Lau, Christopher (NIH/NHGRI) [E]" christopher.lau@nih.gov, Author author@noreply.github.com Subject: Re: [exomiser/Exomiser] Retrospective study (#287)

Hi Chris

I'm not completely clear what you're trying to achieve. Exomiser versions come with their own versioned databases e.g. version 7 ran on a database produced at that time. The software has obviously changed over time too but it would give you an honest snapshot of how things were then.

The exomiser databases are embedded so come as versioned snapshots, but the earliest version available is version 6 from Feb 2015.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/exomiser/Exomiser/issues/287#issuecomment-430641844, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AbegeeW40MStmqIPqpqepm6clJFk5LI0ks5ulzkHgaJpZM4XIaLs.

julesjacobsen commented 6 years ago

@laucc you can download versions 6.0.0 - 11.0.0 from https://data.monarchinitiative.org/exomiser/ These are all snapshots in time both of the software and the data. You can check the release dates for these on the https://github.com/exomiser/Exomiser/releases page.

Versions 6 - 8 have their own bundled data, whereas versions 9+ use a more modular, versioned data which is found in the https://data.monarchinitiative.org/exomiser/data/ directory. These range from Nov 2017 (1711) through to Nov 2018 (1811). So depending on how you wanted to run things you could mix and match the data and software releases over that time period. You might have a few issues with the input commands/ format as these have changed over time, so carefully check the README.md and the example inputs from each release as these illustrate the best way to run the software.

laucc commented 5 years ago

Hi Jules,

Thank you again for your input. We have downloaded the older versions and started to put our cases through.

You mentioned below that Versions 6-8 have their own bundled data. If we understand you correctly, you meant to say we will not be able to use your latest software release to run against data in versions 6 -8. However, we could potentially do this for versions 9+. Is that correct? Please verify.

Thanks for your attention and input. We really appreciate it!

Best regards, Chris

Christopher Lau, PhD, FACMG NIH Undiagnosed Diseases Program, Building 50, Room 5523 MSC 8004 50 South Drive Bethesda, MD 20892-8004 (o) 301 827 4433 (c) 646 300 2308

From: Jules Jacobsen notifications@github.com Reply-To: exomiser/Exomiser reply@reply.github.com Date: Tuesday, November 20, 2018 at 5:37 AM To: exomiser/Exomiser Exomiser@noreply.github.com Cc: "Lau, Christopher (NIH/NHGRI) [E]" christopher.lau@nih.gov, Mention mention@noreply.github.com Subject: Re: [exomiser/Exomiser] Retrospective study (#287)

@laucchttps://github.com/laucc you can download versions 6.0.0 - 11.0.0 from https://data.monarchinitiative.org/exomiser/ These are all snapshots in time both of the software and the data. You can check the release dates for these on the https://github.com/exomiser/Exomiser/releases page.

Versions 6 - 8 have their own bundled data, whereas versions 9+ use a more modular, versioned data which is found in the https://data.monarchinitiative.org/exomiser/data/ directory. These range from Nov 2017 (1711) through to Nov 2018 (1811). So depending on how you wanted to run things you could mix and match the data and software releases over that time period. You might have a few issues with the input commands/ format as these have changed over time, so carefully check the README.md and the example inputs from each release as these illustrate the best way to run the software.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/exomiser/Exomiser/issues/287#issuecomment-440225642, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AbegeSfQtXaxN8pVmjdRmUe7Hx05wwQlks5uw9tCgaJpZM4XIaLs.

julesjacobsen commented 5 years ago

Correct - data version 6-8 cannot be run by software version 9+

laucc commented 5 years ago

Thank you, Jules!

Chris

Christopher Lau, PhD, FACMG NIH Undiagnosed Diseases Program, Building 50, Room 5523 MSC 8004 50 South Drive Bethesda, MD 20892-8004 (o) 301 827 4433 (c) 646 300 2308

From: Jules Jacobsen notifications@github.com Reply-To: exomiser/Exomiser reply@reply.github.com Date: Monday, December 17, 2018 at 9:28 AM To: exomiser/Exomiser Exomiser@noreply.github.com Cc: "Lau, Christopher (NIH/NHGRI) [E]" christopher.lau@nih.gov, Mention mention@noreply.github.com Subject: Re: [exomiser/Exomiser] Retrospective study (#287)

Correct - data version 6-8 cannot be run by software version 9+

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/exomiser/Exomiser/issues/287#issuecomment-447864141, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AbegeRrYRXIck0FOdcVrmcWJjp7Rb7siks5u56nGgaJpZM4XIaLs.