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genome-in-a-bottle / giab_latest_release

This repository contains information about latest release from Genome in a Bottle project
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High Confidence SV calls? #6

Open mozack opened 6 years ago

mozack commented 6 years ago

Is there any set of high confidence structural variant calls available? I do not see any under the giab_latest_release directory.

chunlinxiao commented 6 years ago

Hi Lisle,

GIAB consortium is working on it right now. SVs will be placed in release directory once they are ready.

Thanks

chunlin

From: Lisle Mose [mailto:notifications@github.com] Sent: Tuesday, March 13, 2018 9:47 AM To: genome-in-a-bottle/giab_latest_release giab_latest_release@noreply.github.com Cc: Subscribed subscribed@noreply.github.com Subject: [genome-in-a-bottle/giab_latest_release] High Confidence SV calls? (#6)

Is there any set of high confidence structural variant calls available? I do not see any under the giab_latest_release directory.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHubhttps://github.com/genome-in-a-bottle/giab_latest_release/issues/6, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AM6o1qHgeT8ENL35b03TQtemp0WcabD9ks5td82-gaJpZM4SoteJ.

jzook commented 6 years ago

The current draft "strawman" set of large indel and SV calls for the AJ trio is described here, if you are interested in helping to evaluate them: ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/AshkenazimTrio/analysis/NIST_UnionSVs_12122017/

On Tue, Mar 13, 2018 at 10:17 AM chunlinxiao notifications@github.com wrote:

Hi Lisle,

GIAB consortium is working on it right now. SVs will be placed in release directory once they are ready.

Thanks

chunlin

From: Lisle Mose [mailto:notifications@github.com] Sent: Tuesday, March 13, 2018 9:47 AM To: genome-in-a-bottle/giab_latest_release < giab_latest_release@noreply.github.com> Cc: Subscribed subscribed@noreply.github.com Subject: [genome-in-a-bottle/giab_latest_release] High Confidence SV calls? (#6)

Is there any set of high confidence structural variant calls available? I do not see any under the giab_latest_release directory.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub< https://github.com/genome-in-a-bottle/giab_latest_release/issues/6>, or mute the thread< https://github.com/notifications/unsubscribe-auth/AM6o1qHgeT8ENL35b03TQtemp0WcabD9ks5td82-gaJpZM4SoteJ>.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/genome-in-a-bottle/giab_latest_release/issues/6#issuecomment-372680588, or mute the thread https://github.com/notifications/unsubscribe-auth/ACU6drmXElAd3fQlb0v3VtdJsQBtGfnqks5td9T_gaJpZM4SoteJ .

mozack commented 6 years ago

Thanks, I'll take a look.

eroller commented 5 years ago

Where can I find SV calls for NA12878?

chunlinxiao commented 5 years ago

Hi Eric,

GIAB consortium does not have high-confidence SV calls for NA12878 yet at this moment.

Thanks

chunlin

From: Eric Roller notifications@github.com Sent: Wednesday, January 02, 2019 3:01 PM To: genome-in-a-bottle/giab_latest_release giab_latest_release@noreply.github.com Cc: Xiao, Chunlin (NIH/NLM/NCBI) [E] xiao2@ncbi.nlm.nih.gov; Comment comment@noreply.github.com Subject: Re: [genome-in-a-bottle/giab_latest_release] High Confidence SV calls? (#6)

Where can I find SV calls for NA12878?

— You are receiving this because you commented. Reply to this email directly, view it on GitHubhttps://github.com/genome-in-a-bottle/giab_latest_release/issues/6#issuecomment-450968714, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AM6o1p8n3c4SGbAlfFOHEyoUHlmyn-18ks5u_Q__gaJpZM4SoteJ.