Notice:
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We appreciate your help!

Test-drive the GATK tools and Best Practices pipelines on Terra


Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

readbackedphasing (HaplotypeCaller) outputs much more 0|1 then 1|0, why?

amyamy SwedenMember

Hi!

With the aim of phasing haplotype from SNPs of a single individual, I have used HaplotypeCaller which performes ReadBackedPhasing automatically (accuracy of SNP calling is beyond the question). However I observed much more 0|1 (98%, among all phased heterozygous SNPs) then 1|0 (2%).

What I don't understand is that as the reference is built from a mixing of diploid genome, when a output haplotype in .vcf start with 0|1, the next SNP should by chance have 50% of probability to be 0|1 and 50% to be 1|0. In another word, because the reference is unphased haplotype, then when I phase SNPs against such reference, I should have similar amount 0|1s and 1|0s.

For example, in any phased haplotype containg 2 SNPs, for the 1st SNP it always starts with 0|1. For the 2nd SNP, I expect to have similar amount of 0|1 and 1|0. But I have much more 0|1 then 1|0.

I have tried datasets from 5 different species and multiple individuals, including human, birds, and fish. The results are very similar.

I think I may have some misunderstanding about readbackedphasing. Can anyone help me with that?

Thanks.

Best Answer

Answers

  • YingLiuYingLiu ChinaMember

    @Geraldine_VdAuwera
    suppose I got the HP mark from RBP :
    1001-1 ,1001-2
    the genotype is 0|1
    I do not know what 's the meanning of '-1' and '-2' ,
    but I guess '-1' means this allele is located at forward strand from A chrosome , '-2' means rever strand from B chrosome.
    it 's right ?

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    @YingLiu
    Hi,

    Have a look at Menachem's answer here.

    -Sheila

  • YingLiuYingLiu ChinaMember

    @Sheila
    thank you! it is the answer I want .
    also thanks to @fromer

    The interpretation of:
    GT:GQ:HP 0/1:99:17690409-1,17690409-2
    GT:GQ:HP 0/1:99:17690409-2,17690409-1:1258.14

    is indeed as @npontikos takes it to mean:

    The second site's alternate allele (1) is on the same physical haplotype as the first site's reference allele (0), and vice versa [second site's 0 goes with first site's 1]. This is based on the fact that the HP pairs line up in reverse order between these two genotypes.

    And, indeed, in the old notation that RBP used to output, this would have been:
    0/1
    1|0

    The reason we changed this is for multiple reasons of (ambiguity, incompleteness, possible inconsistency with trio-based phasing), where the HP tag more explicitly links up alleles at (perhaps non-consecutive) genotypes of the same sample.

  • YingLiuYingLiu ChinaMember

    @Sheila @fromer
    another question ,all sites with common same HP tag are located at a same read ?
    or the same haplotype equal to same read ?

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    @YingLiu
    Hi,

    I think the article above the thread I linked to will help.

    -Sheila

  • YingLiuYingLiu ChinaMember

    @Sheila said:
    @YingLiu
    Hi,

    I think the article above the thread I linked to will help.

    -Sheila

    @Sheila Hi, this link I think it can't answer my quesition ...
    all sites with common same HP tag are located at a same read ?
    or the same haplotype equal to same read ?

    RBP just phase SNPs , I am not sure whether current GVCF can phase both SNPs and INDELs ?
    thank you !

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    @YingLiu
    Hi,

    They are on the same haplotype.

    HalotypeCaller can phase both indels and SNPs.

    -Sheila

Sign In or Register to comment.