Yutang Chen

Thank you so much for your great explanation, Pasi. I will try my best to digest what you wrote. Best wishes, Yutang

Great, Pasi. Thank you so much for your very helpful reply. Maybe I should have separated the last three questions from my first question to make my last three questions not related to the first one. For the first question, I totally agree with you. For the 4th question, thanks for elaborating on sexAveraged=1. Now I got it. Now for question 2 and 3, actually it is not about the sex status of the parents in the pedigree file (the parental-sex status of the individuals was assigned to 0), it is more...

Dear Pasi, Long time no see, and I hope you are well. I have some questions regarding consensus map. I wish you could share your brilliant input here with us. First, some background of what we have done: * We did reciprocal crossing between two heterozygous parents. The parents are allogamous forage grasses, and let's call them P1 and P2. * We collected seeds from both parents, resulting in ~300 F1 individuals. * We sequenced these F1 plants together with the parental plants using genotyping-by-sequencing...

Dear Pasi, I hope you are well. It seems my last reply to your last respond didn't get posted. So here I write to you again. Yes, you are absolutely right. To determine the phase among linkage groups in one parent, data of grandparents are needed. Actually, my question should be whether the first haplotype in the phased parental genotypes is consistently grandmother or grandfather haplotype among linkage groups. Thank you very much for your help, and please have a nice week. Best wishes, Yutang

Dear Pasi, I have another question: is the first haplotype consistently the mother or father haplotype among linkage groups? Thank you very much. Best wishes, Yutang

Dear Pasi, Just want to let you know, with the Lep-MAP3 variant calling pipeline, I successfully got the parental phase! By the way, just want ask, would the phase change if I order the markers based on the given order? Or, the other way around, I used the given order (order from base pair position) to order the markers, if I don't use a given order, would the phase be different? Thank you very much. Best wishes, Yutang

Never mind, Pasi, I am running your variant calling pipeline now. I will get back to you when I get the results. Best wishes, Yutang

Dear Pasi, I think I need your help now. I have the vcf file generated by bcftools as input, and the parental genotypes I got from OrderMarkers2 are all AC or CA. I guess this is because as you said you just convert 0,1,2,3 to A,C,G,T, respectively, even though 0 or 1 might not really correspond to A or C. So, if I want to get genotypes with the correct ACGT codes, then I have to follow the Lep-MAP3 variant calling pipeline. Is this right? Can I convert vcf file to the genotype likelihoods? Thank...