Question

Does anyone know what exactly 1/2 mean?

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6.3 years ago

hananreda232 • 0

Does anyone know what exactly genotype 1/2 mean?

SNP

Thank you!

SNP • 1.2k views

ADD COMMENT • link updated 6.3 years ago by pschnepp • 0 • written 6.3 years ago by hananreda232 • 0

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It can mean many things, a bit of context would help.

ADD REPLY • link 6.3 years ago by Devon Ryan 104k

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it's 0.5 ? (but I'm not sure about this...)

ADD REPLY • link 6.3 years ago by Pierre Lindenbaum 161k

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it's a unphased variant with both alleles (maternal and paternal) known. sign / is for unphased variant and 1 and 2 are alternate alleles of this variant compared to reference. It is a heterozygous allele.

ADD REPLY • link 6.3 years ago by cpad0112 21k

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He knows. He was kidding.

ADD REPLY • link 6.3 years ago by Ram 43k

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I know. :). 1/2=0.5. My post was supposed to be comment to OP. Instead it became sub post to Pierre's post. I tried making comment to top post (OP), could not.

ADD REPLY • link 6.3 years ago by cpad0112 21k

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Delete + repost maybe?

ADD REPLY • link 6.3 years ago by Ram 43k

score 4 · Answer 1 · 2017-12-19

The reference has a certain base. The SNP data show two different bases (1 and 2) on that position. Basically, it could happen if the reference has an A but the reads you align, and with which you do the calling, have either a G or a C. Obviously, it works also with all the other three genome bases.

Sites where you have 1|2 are the ones that are heterozygous and both different from the reference. They're not common, so they're usually really interesting because it means that that position has a high variation level in the population. Obviously, I would first check the allelic fraction of both 1 and 2, because maybe only one read is confirming genotype 2, and all the others are of genotype 1. This would mean that it is likely a sequencing error. :)

score 0 · Answer 2 · 2017-12-22

Also take a look at how many variant alleles are in the final vcf file. I've had Gatk call multiple variant calls after merging multiple samples to do joint calling (following gatk best practices recommendation). Usually the reference all is labeled 0 and 1 or 2 would refer to a variant allele. Your SNP site might have two variant alleles. I would recommend checking your samples at this site to make sure it's not a sequencing error for one of your samples. It could be one sample had a amplification error that propagated throughout and isn't a true variant.