search

Clinical-Genomics / BALSAMIC

Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer
https://balsamic.readthedocs.io/
MIT License
44 stars 16 forks source link

Include the analysis of signatures and MSI #972

Open terestahl opened 2 years ago

terestahl commented 2 years ago

Hi I wonder if it is possible to include in balsamic pipeline the analysis of signatures and MSI This is important for some pediatric cases

thanks

teresita

northwestwitch commented 2 years ago

Moved from Scout to Balsamic!

khurrammaqbool commented 10 months ago

@terestahl Could you please elaborate on "analysis of signatures". It will be helpful if tools and/or references are included as well.

terestahl commented 10 months ago

When did I write this? in the context of balsamic analysis? Or what are your ideas for integrating tools in balsamic? Please let me know and then I can be more specific teresita

From: Khurram Maqbool @.> Sent: den 1 november 2023 10:40 To: Clinical-Genomics/BALSAMIC @.> Cc: Teresita Díaz De Ståhl @.>; Mention @.> Subject: Re: [Clinical-Genomics/BALSAMIC] Include the analysis of signatures and MSI (Issue #972)

@terestahlhttps://github.com/terestahl Could you please elaborate on "analysis of signatures". It will be helpful if tools and/or references are included as well.

- Reply to this email directly, view it on GitHubhttps://github.com/Clinical-Genomics/BALSAMIC/issues/972#issuecomment-1788672140, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ARWZPHYTVVDIDOYD3OQPYGTYCIKF3AVCNFSM5Z6INMAKU5DIOJSWCZC7NNSXTN2JONZXKZKDN5WW2ZLOOQ5TCNZYHA3DOMRRGQYA. You are receiving this because you were mentioned.Message ID: @.**@.>>

När du skickar e-post till Karolinska Institutet (KI) innebär detta att KI kommer att behandla dina personuppgifter. Här finns information om hur KI behandlar personuppgifterhttps://ki.se/medarbetare/integritetsskyddspolicy.

Sending email to Karolinska Institutet (KI) will result in KI processing your personal data. You can read more about KI's processing of personal data herehttps://ki.se/en/staff/data-protection-policy.

khurrammaqbool commented 10 months ago

@terestahl This is an issue in BALSAMIC repository.

terestahl commented 10 months ago

MSI (Microsatellite instability) for example is integrated in Sarek, you can probably find the reference in Sarek documentation MSI determination functions for WGS (not for WES) For the few pediatric samples that showed HIGH MSI it was in accordance to the findings from the MOLPAT lab

Regarding Signatures I was referring to cosmic signatures which I have succeeded in installing in our server and it is useful when one suspects mismatch repair defects @.*** It is also useful to calculate BRACness, but that I have not tried but I think there is a nature paper from 2017 with the documentation, I do not find it now

Al these are useful

Thanks

teresita

From: Khurram Maqbool @.> Sent: den 1 november 2023 10:51 To: Clinical-Genomics/BALSAMIC @.> Cc: Teresita Díaz De Ståhl @.>; Mention @.> Subject: Re: [Clinical-Genomics/BALSAMIC] Include the analysis of signatures and MSI (Issue #972)

This is an issue in BALSAMIC repository.

- Reply to this email directly, view it on GitHubhttps://github.com/Clinical-Genomics/BALSAMIC/issues/972#issuecomment-1788685275, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ARWZPH7AQ5UHEL5HMC6GQIDYCILORAVCNFSM5Z6INMAKU5DIOJSWCZC7NNSXTN2JONZXKZKDN5WW2ZLOOQ5TCNZYHA3DQNJSG42Q. You are receiving this because you were mentioned.Message ID: @.***>

När du skickar e-post till Karolinska Institutet (KI) innebär detta att KI kommer att behandla dina personuppgifter. Här finns information om hur KI behandlar personuppgifterhttps://ki.se/medarbetare/integritetsskyddspolicy.

Sending email to Karolinska Institutet (KI) will result in KI processing your personal data. You can read more about KI's processing of personal data herehttps://ki.se/en/staff/data-protection-policy.