question about the outputs

[jaewon-cho]

Hello ctat team,
I am trying CTAT v3.2.0.
After I run it, there were ~.vcf.gz and ~.XGBoost-classifier.vcf.gz.

I think the raw GATK result is ~.vcf.gz
(If I am looking for the variants from the normal cell (not the cancer cell), does this file is good to use?)
and
~.XGBoost.classifier.vcf.gz
is filtered by some criteria
what is the meaning of this result?

(P.S. Does XGBoost-classifier.cancer.vcf indicates the result of variants classified into cancer mutation?)

[brianjohnhaas]

hi, The XGBoost involves a refined variant selection, generally increasing overall prediction accuracy from the regular gatk results. The cancer.vcf includes those variants that are further predicted to be pathogenic.

…

On Mon, Nov 15, 2021 at 9:16 PM jaewon-cho ***@***.***> wrote: Hello ctat team, I am trying CTAT v3.2.0. After I run it, there were ~.vcf.gz and ~.XGBoost-classifier.vcf.gz. I think the raw GATK result is ~.vcf.gz and ~.XGBoost.classifier.vcf.gz is filtered by some criteria what is the meaning of this result? (P.S. Does XGBoost-classifier.cancer.vcf indicates the result of variants classified into cancer mutation?) — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#102>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABZRKX3SSTXQE5QMWTBR753UMG5G7ANCNFSM5IDD6VTA> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.

-- -- Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas <http://broad.mit.edu/~bhaas>

[jaewon-cho]

Thank you for your kind response