iCHOR on any Genome

[PedalheadPHX]

https://github.com/tgen/phoenix/blob/0e6f1e256e5f23907e81d136c0b27b1d4b2df9a5/modules/germline/main.jst#L43

After talking with Murtaza, I think to support cfDNA, and quality control efforts we should run iCHOR on all genomes. But the results for a constitutional should go to the constitutional copy number folder and results for a tumor to the somatic copy number folder.

[ryanrichholt]

Fixed this with: 50d3ddeaab7381d29a1e057a0194b6e0dd2a5bab

@PedalheadPHX It's still running for exome samples, without any exome specific tuning. Should I turn it off completely for exome samples?

[PedalheadPHX]

Yes just one genomes

On Thu, May 2, 2019 at 10:50 Ryan Richholt notifications@github.com wrote:

Fixed this with: 50d3dde https://github.com/tgen/phoenix/commit/50d3ddeaab7381d29a1e057a0194b6e0dd2a5bab

@PedalheadPHX https://github.com/PedalheadPHX It's still running for exome samples, without any exome specific tuning. Should I turn it off completely for exome samples?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/tgen/phoenix/issues/86#issuecomment-488767891, or mute the thread https://github.com/notifications/unsubscribe-auth/AC6VCHDXNFR23V56VIHP3NTPTMSVTANCNFSM4HJOIABQ .

-- Sent from a mobile device

--

This electronic message is intended to be for the use only of the named recipient, and may contain information that is confidential or privileged, including patient health information. If you are not the intended recipient, you are hereby notified that any disclosure, copying, distribution or use of the contents of this message is strictly prohibited. If you have received this message in error or are not the named recipient, please notify us immediately by contacting the sender at the electronic mail address noted above, and delete and destroy all copies of this message. Thank you.

[ryanrichholt]

201ee93