GT value in VCF files of a haplotype species.

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4.2 years ago

Andrew Liu ▴ 10

Hi, I'm now working on calling variants from Chlamydomonas, Cuz' Chlamydomonas is a haplotype species, so what's the meaning of GT in VCF files? Can I regard 0/0 as homozygote? Thanks!

WGS genetics • 919 views

ADD COMMENT • link 4.2 years ago by Andrew Liu ▴ 10

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What Does Genetype ("0/0", "0/1" Or "1/1") In *.Vcf File Represent? ; Why is 0/0 homozygous reference call in VCF useful information? ; VCF Files: Help on 0/1 1/1 0/0 1/1 | vs / (phased & unphased ; etc...

ADD REPLY • link 4.2 years ago by Pierre Lindenbaum 164k

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Thanks for you reply. But Chlamydomonas is a haplotype species, so I'm wondering what if I got 1/1, what's the meaning of the result? Does it mean the both of chains of DNA are changed?

ADD REPLY • link 4.2 years ago by Andrew Liu ▴ 10

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. But Chlamydomonas is a haplotype species, so I'm wondering what if I got 1/1,

do you mean haploid ?

so it's more a problem with your variant caller than with the vcf format itself.

ADD REPLY • link 4.2 years ago by Pierre Lindenbaum 164k

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