Yutang Chen

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...

Dear Pasi, Very happy to hear from you! Two days ago, I was just too excited thinking that it might be a good idea to add a separator. Now, after reading more carefully of the new features, I realized that there is no need to add a separator between alleles. Just now, I was about to write to tell you to ignore what I said, but I found you already replied. Very sorry and always appreciate your quick response and support! I will try the new scripts first and update you what I find. Again, great job!...

Dear Pasi, I hope you are well. It has been more than one year since we last met at PAG where we shortly discussed generating parental phase. I was just reading the Summary page of Lep-MAP3 and I found in the second picture of Project Samples, you actually added a column of parental phase in the output file of ordermarkers2! This is so great! Thank you very much. One thing I would like to confirm is, for example, in the mother phased genotype, is it true that alleles at the left or right side belong...

Hi Pasi, I hope you are well. I read from the wiki under the ParentalCall section, you said "Other kind of variants (like indels) can be given as input by specifying them as SNPs (e.g. AA=homozygote indel, AT=heterozygote indel, TT=no indel)". Does this mean that I have to manually specify indels in vcf file as SNPs or does lepmap3 can automatically convert indels in vcf to SNPs? I got confused there, could you please give me some hints? If I need to manually specify indels as SNPs, how could I do...