<INV> calls showing wrong values of AF

[yashcrux]

Hello I have attached here a snapshot of the CAMPHORsomatic output

Here all the SV calls show an allele Frequency which I am unable to understand.

Is it expected or a bug?

[afujimoto]

Thank you four your email This should be caused by a bug of my script. I am sorry. Vcf file is generated from 5 files (somatic_DEL_candidate_filtered.txt somatic_INS_candidate_filtered.txt somatic_INV_candidate_filtered.txt somatic_TRS_candidate_filtered.txt somatic_CHR_candidate_filtered.txt). I would be grateful if you show me a format of these files.

Regards,

Akihiro

2023/06/29 22:48、yashcrux @.***>のメール:

Hello I have attached here a snapshot of the CAMPHORsomatic output https://user-images.githubusercontent.com/61901132/249789043-e645ad2f-0879-463d-80a2-477dcb240e90.png Here all the SV calls show an allele Frequency which I am unable to understand.

Is it expected or a bug?

— Reply to this email directly, view it on GitHub https://github.com/afujimoto/CAMPHORsomatic/issues/7, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADFCBLR46GOF7F3QRVSVZV3XNWBTTANCNFSM6AAAAAAZYRNBFU. You are receiving this because you are subscribed to this thread.

[yashcrux]

Hi Thanks for your reply. I'll send you the INV file attached here for one of our in-house somatic_INV_candidate_filtered_m54274Ue_220414_145454_m54274Ue_221001_133159.txt sample

[afujimoto]

Thank you for the file. Based on the read name, the data seems to be PacBio. Our script was originally developed for analysis of Nanopore. Recently, our collaborators started to use our method for PacBio, and they modified our script for PacBio. I will analyze our PacBio data with the original script and the modified script, and will tell you the result. If the modified script run well for PacBio and Nanopore, I will upload the script ASAP.

2023/06/30 17:09、yashcrux @.***>のメール:

Hi Thanks for your reply. I'll send you the INV file attached here for one of our in-house somatic_INV_candidate_filtered_m54274Ue_220414_145454_m54274Ue_221001_133159.txt https://github.com/afujimoto/CAMPHORsomatic/files/11914272/somatic_INV_candidate_filtered_m54274Ue_220414_145454_m54274Ue_221001_133159.txt sample

— Reply to this email directly, view it on GitHub https://github.com/afujimoto/CAMPHORsomatic/issues/7#issuecomment-1614292126, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADFCBLXV6USHNHM34H3IBKLXN2CURANCNFSM6AAAAAAZYRNBFU. You are receiving this because you commented.

[yashcrux]

Hi Thanks for letting me know this.

Are there any further updates now!