PyPGx supports targeted sequencing data

[sbslee]

The main purpose of this discussion is to let people know that PyPGx supports targeted sequencing data (in addition to data from WGS, WES, SNP array, and long-read sequencing) for PGx genotyping including structural variation detection. For example, I recently published a paper where I applied PyPGx to the ClinPharmSeq data (ClinPharmSeq: A targeted sequencing panel for clinical pharmacogenetics implementation).

Relevant resources:

• Overview of NGS pipeline from PyPGx
• List of 59 PGx genes targeted by PyPGx

[sbslee]

@AnnaGreenOrebro, I saw your recent post asking whether Cyrius is planning to support targeted sequencing data. Have you tried PyPGx? I'm asking here because I didn't want to hijack the discussion :)

[sbslee]

Adding @yafengwen.

[yafengwen]

@sbslee , Thanks a lot for sharing!
We have a small sample size of targeted sequencing data for PGx and I am comparing the results from different bioinformatics tools to the traditional genotyping method. It would be interesting to try PyPGx as well!

[sbslee]

Adding @neoscreen.

[sbslee]

Adding @aroon-color from the Aldy repository.

[sbslee]

Also @anh151 and @deb0612.

[AnnaGreenOrebro]

Thanks! I will try, kind of you! Anna Från: sbslee ***@***.***> Skickat: den 24 augusti 2022 07:26 Till: sbslee/pypgx ***@***.***> Kopia: Green Anna, Klinisk genetik ***@***.***>; Mention ***@***.***> Ämne: Re: [sbslee/pypgx] PyPGx supports targeted sequencing data (Discussion #70) @AnnaGreenOrebro<https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FAnnaGreenOrebro&data=05%7C01%7Canna.green%40regionorebrolan.se%7C7cdae2c784e54f06e52f08da8591237d%7Caece5b1982274c2782181aea120ec062%7C0%7C0%7C637969155655725467%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=I%2BcY9Mi6IqzbqfEe2G03KC0jwHeOqX%2FtGP29jokqn5w%3D&reserved=0>, I saw your recent post asking whether Cyrius is planning to support targeted sequencing data. Have you tried PyPGx? I'm asking here because I didn't want to hijack the discussion :) — Reply to this email directly, view it on GitHub<https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fsbslee%2Fpypgx%2Fdiscussions%2F70%23discussioncomment-3462248&data=05%7C01%7Canna.green%40regionorebrolan.se%7C7cdae2c784e54f06e52f08da8591237d%7Caece5b1982274c2782181aea120ec062%7C0%7C0%7C637969155655725467%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=NiH9%2BFnP1VScExzHk3t2ipKFWoGkWvrl6cZevqrlD1g%3D&reserved=0>, or unsubscribe<https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FALVM2PHMGS2AIUUTGQPJR3LV2WW6VANCNFSM57N33NPA&data=05%7C01%7Canna.green%40regionorebrolan.se%7C7cdae2c784e54f06e52f08da8591237d%7Caece5b1982274c2782181aea120ec062%7C0%7C0%7C637969155655881191%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=eNGz26abVPNdFAqNXo9TzciXuSBMw0bUl%2BJewQjs%2Fag%3D&reserved=0>. You are receiving this because you were mentioned.Message ID: ***@***.******@***.***>>