Hello guys! i have a simple question about interpreting the following outputs. 1) So my question is if someone can explain to me just by looking at the GT section of the vcf file i can say which allel comes from which parent or if this is a denovo. Maybe another commented example step by step could help. 2) My problem is that i still dont know when a sample is homozygous or not just by this outputfile 3) What does Incomp specifically mean in this example?
Thanks to everyone helping me understanding this task --MediumHeat
ID=NA12451,Sex=FEMALE,Affectionstatus=1,
ID=NA12452,Sex=MALE,Affectionstatus=0,
ID=NA12453,Sex=FEMALE,Affectionstatus=0,
1) 1:1529817 G->C rs4075275 2|1, 2|2, 2|2 1:1529817G> HOM:1 FAT:t MOT:t INCOMP:0
2) 1:746243 T->A,C,G 2|1, 0|1, 2|3 1:746243T>G HOM:0 FAT:f MOT:f INCOMP:0 (de-novo) 1:746243T>C HOM:0 FAT:t MOT:f INCOMP:1
Those are not VCF lines, it is hard to see the allele assignation without the header line