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moka-guys / moka-fe

This repo is incomplete and serves as a backup of some code from Moka. It includes some legac(hitt)y code.
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56G pipeline #270

Closed nfoot closed 6 years ago

nfoot commented 7 years ago

Currently we are using a manual process, which is in the development stage, for analysis of teh Swift 56 gene panel. The flanking file is a work in progress. We have done two runs so far.

We are aiming to bring this into diagnostics early next year and the clinicians are keen this is moved forward in a timely fashion.

Please can an automatic pipeline be developed that is similar to the Swift 5 panel - that can run on the cloud and pass teh VCFs directly to Ingenuity.

If Moka will need some amendments to deal with teh 56G VCFs then please can this also be done.

Thanks Nicky

woook commented 7 years ago

Dear Nicky

Please could this be taken to the R&D meeting for setting a priority.

Thanks,

Wook

From: nfoot [mailto:notifications@github.com] Sent: 15 September 2017 15:41 To: woook/moka-fe moka-fe@noreply.github.com Cc: Subscribed subscribed@noreply.github.com Subject: [woook/moka-fe] 56G pipeline (#270)

Currently we are using a manual process, which is in the development stage, for analysis of teh Swift 56 gene panel. The flanking file is a work in progress. We have done two runs so far.

We are aiming to bring this into diagnostics early next year and the clinicians are keen this is moved forward in a timely fashion.

Please can an automatic pipeline be developed that is similar to the Swift 5 panel - that can run on the cloud and pass teh VCFs directly to Ingenuity.

If Moka will need some amendments to deal with teh 56G VCFs then please can this also be done.

Thanks Nicky

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nfoot commented 7 years ago

Sure - I have submitted it now so there is a formal request for consideration ahead of the R&D meeting.

Same goes for the coverage report request.

Thanks

Nicola Foot DipRCPath| Viapath Operations Lead, Cancer Genetics Genetics Department|5th Floor Tower Wing| Guy's Hospital| London SE1 9RT 0207 188 1716 nicola.foot@viapath.co.ukmailto:nicola.foot@viapath.co.uk www.viapath.co.ukhttp://www.viapath.co.uk/

From: woook [mailto:notifications@github.com] Sent: 15 September 2017 15:43 To: woook/moka-fe Cc: Foot Nicola; Author Subject: Re: [woook/moka-fe] 56G pipeline (#270)

Dear Nicky

Please could this be taken to the R&D meeting for setting a priority.

Thanks,

Wook

From: nfoot [mailto:notifications@github.com] Sent: 15 September 2017 15:41 To: woook/moka-fe moka-fe@noreply.github.com Cc: Subscribed subscribed@noreply.github.com Subject: [woook/moka-fe] 56G pipeline (#270)

Currently we are using a manual process, which is in the development stage, for analysis of teh Swift 56 gene panel. The flanking file is a work in progress. We have done two runs so far.

We are aiming to bring this into diagnostics early next year and the clinicians are keen this is moved forward in a timely fashion.

Please can an automatic pipeline be developed that is similar to the Swift 5 panel - that can run on the cloud and pass teh VCFs directly to Ingenuity.

If Moka will need some amendments to deal with teh 56G VCFs then please can this also be done.

Thanks Nicky

- You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHubhttps://github.com/woook/moka-fe/issues/270, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AFdGYsrFgHu5uHVHtRReurwIp8gEO4vFks5sioyWgaJpZM4PZE6g.

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woook commented 6 years ago

Taken to R&D.