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 to the same haplotype? Normally in vcf file, the phased genotype is present with a vertical bar separator, for example, A|T, and the unphased genotype is coded as A/T. Maybe I am too greedy, but in the future update, is it OK to add a separator between alleles?
I will download the new package and try to get the parental phase for our data. Thank you very much for your brilliant work, and I will get back to you to report my results.
Best wishes,
Yutang
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Nice to hear from you. And thanks for the suggestion, the phase information has been very useful. I added it soon after the PAG meeting where we discussed it.
I have used the phase for so many projects, that I would not want to change the format anymore. There is the vcfPhase.awk script (in scripts.zip) that adds "|" between alleles for vcf input (AT=>0|1). This could be modified to change AT=>A|T. Note that the ACGT codes are correct only for the Lep-MAP3 variant calling. For vcf input, numeric values 0,1,2,3 are converted A,C,G,T, respectively. The numeric codes can be non-SNP variants as well.
And yes, the maternal and paternal genotypes are phased for the entire linkage group. First alleles form one haplotype as well as the second alleles.
Cheers,
Pasi
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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!
Best wishes,
Yutang
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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 you very much,
Yutang
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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
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In the phase information, first there is the paternal phased genotype (e.g. GA) and then, separated by "," is the maternal one (each family separated by ";"). The two haplotypes are in arbitrary order (but you know that they are the fathers two haplotypes and the mothers two haplotypes). If you use grandparents for phasing, then the first is inherited from the parent's father and second from the parent's mother.
Cheers,
Pasi
Last edit: Pasi Rastas 2024-04-05
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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
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
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 to the same haplotype? Normally in vcf file, the phased genotype is present with a vertical bar separator, for example, A|T, and the unphased genotype is coded as A/T. Maybe I am too greedy, but in the future update, is it OK to add a separator between alleles?
I will download the new package and try to get the parental phase for our data. Thank you very much for your brilliant work, and I will get back to you to report my results.
Best wishes,
Yutang
Dear Yutang,
Nice to hear from you. And thanks for the suggestion, the phase information has been very useful. I added it soon after the PAG meeting where we discussed it.
I have used the phase for so many projects, that I would not want to change the format anymore. There is the vcfPhase.awk script (in scripts.zip) that adds "|" between alleles for vcf input (AT=>0|1). This could be modified to change AT=>A|T. Note that the ACGT codes are correct only for the Lep-MAP3 variant calling. For vcf input, numeric values 0,1,2,3 are converted A,C,G,T, respectively. The numeric codes can be non-SNP variants as well.
And yes, the maternal and paternal genotypes are phased for the entire linkage group. First alleles form one haplotype as well as the second alleles.
Cheers,
Pasi
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!
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 you very much,
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,
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
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 Yutang,
In the phase information, first there is the paternal phased genotype (e.g. GA) and then, separated by "," is the maternal one (each family separated by ";"). The two haplotypes are in arbitrary order (but you know that they are the fathers two haplotypes and the mothers two haplotypes). If you use grandparents for phasing, then the first is inherited from the parent's father and second from the parent's mother.
Cheers,
Pasi
Last edit: Pasi Rastas 2024-04-05
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 Yutang,
Yes, it is consistent.
Cheers,
Pasi