Is it possible to get haplotype sequences for samples from a vcf SNP file and a reference sequence?

vschillingvschilling toulouseMember

Hi, I would like to know if it is possible to get haplotype sequences for samples from a vcf SNP file and a reference sequence. The fact is that I took back from a paper a vcf file and a reference sequence, but I don't have bam files. The only solution I see is to ask for bam files...
Thanks in advance,

vschill

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  • vschillingvschilling toulouseMember

    Hi Sheila,
    thanks for your answer, I will try to ask for them.

    vschill

  • vschillingvschilling toulouseMember

    Hi, thanks very much Geraldine, I will try it !

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    @vschilling
    Hi Vschill,

    I talked with Geraldine after she made the recommendation, and it seems we are both not sure what exactly you want. The most common use case (which Geraldine assumed you were asking about) is that people have a vcf for a specific haplotype that they want to produce, and they just want to incorporate the variants as they are in the VCF, into the reference sequence. Is that what you are asking for? If not, there are several options depending on whether your organism is haploid, diploid or polyploid, what exactly you have in your vcf, etc.

    I thought you were asking about having Haplotype Caller output the artificial haplotypes. For that, you will need the bam files.

    -Sheila

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