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bioinform / somaticseq

An ensemble approach to accurately detect somatic mutations using SomaticSeq
http://bioinform.github.io/somaticseq/
BSD 2-Clause "Simplified" License
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Question for the paper on establishing the reference call set #119

Closed FriederikeHanssen closed 1 year ago

FriederikeHanssen commented 1 year ago

Hi!

I have recently read both papers on Establishing the reference call set and about the Best-practices and found them really interesting and helpful. We discussed the methods and I had a question for the WGS part of the reference call set: As far as I understood you used PCR-free kits for it, right? Did you also use any of the WGS datasets with PCR for the reference call set?

Best and thank you! :)

litaifang commented 1 year ago

No, we did not. Basically we used the best sequencing data we could get to establish the reference. Datasets with PCR is only used to see how it compares with the more sample-demanding PCR-free sequencing.

litaifang commented 1 year ago

To clarify an earlier typo, no we did not use anything other than PCR-free WGS data sets to establish the high-confidence call set.

FriederikeHanssen commented 1 year ago

Hi! Thank you very much for clarifying :)