What is the tlod in vcf?
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2.2 years ago
2yuna710 ▴ 10

Hi, I have some questions related to tlod in vcf file.

Please explain what I wonder.

  1. I don't know exactly tlod in vcf file. I made vcf files by MuTect2 of GATK. If I read that file, it shows data (i.g. TLOD=1007.42). What is tlod?? Is it tumor log odds ratio or tumor likelihood ratio? And how do the tool calculate tlod? If the data is log, TLOD=1007.42 means too big number.

  2. I want to get the reason why the default TLOD filtration cutoff is 6.3.

GATK MuTect2 tlod • 1.1k views
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it should be defined in the VCF header. grep "^#" vcf | grep TLOD

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