Double Alt Heterozygous Variant In Vcf?

Question

[nmb]

Was wondering how VCF denotes a heterozygous variant in which both alleles are different from the reference? E.g.: A to G/T.

I know how to express A > G/A or A > G/G, but wasn't able to find an explanation for the above the spec. I may have also been looking in the wrong place. Thanks in advance!

[Shicheng Guo]

bcftools norm -m-snps: will turn G,T to two lines.

bcftools norm -m+snps: will turn two lines to one line and separte with ,

bcftools norm -m-snps dbSNP153.hg19.vcf -Ov -o dbSNP153.hg19.norm.vcf

Answer 1

[Pierre Lindenbaum]

Was wondering how VCF denotes a heterozygous variant in which both alleles are different from the reference? E.g.: A to G/T.

you'll find A in the REF column and G,T in the ALT column

"ALT : comma separated list of alternate non-reference alleles called on at least one of the samples"

[nmb]

Thanks, makes sense! To answer a bit of my own question, it looks like the sample column would have 1/2 in that case to denote the allele.