GT value in VCF files of a haplotype species.
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6 months 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 • 183 views
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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?

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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.

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