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I am working in a exome sequencing project in family trios. I have used all the Best Practices to analyze the sequences. I ran the PhaceByTransmission walker with the ‘’MendelianViolationsFile flag hoping that the generated Mendel violation filed would give me information about the possible de novo variants. Nonetheless, I did not understand what the columns of the output file mean. Could you please help me to understand the file’s nomenclature?
I also tried to extract the de novo variants using an in house script but I am not sure about the nomenclature of the phased .vcf file. I would like to know the difference between ./. , 1/0, 0/1 and 1/1 among the three family members. For example, I obtained 0/1 ./. ./. (for child, mother, father) but I do not know if I extract this row, this might represent a de novo variant.
Thank you for your time