Comments (2)
Glad you found it useful. The two tumor alleles are meant to indicate zygosity in the sample. This is determined from the GT entry in the vcf genotype column for the appropriate sample. Or from the variant allele fraction if GT was unavailable. If GT or allele depths are not available in the vcf, then heterozygosity is assumed... i.e. Tumor_Seq_Allele1 will be set to the reference allele.
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That makes perfect sense. I've just never come across a file format that encoded for zygosity before. That's good to know. Thanks for clarifying!
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