brianjohnhaas
commented
2 years ago 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?)
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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?)