VCF files columns-biological explanation.

Question

[GK1610]

I am working on joint genotype call of gvcf files of 200 samples. This is my first time with vcf data. I get the format. but I am struggling with some basic questions like

What is a reference allele e.g. in hg19 file from 1000 genomes_phase3? Is it the reference allele seen on most of people sequence?

What is an alternate allele? Is it the one which is minor allele at that variant and position?

What is NON_REF allele in alt. allele column?

Answer 1

[WouterDeCoster]

The reference genome is a combination of individuals which got sequenced to generate one haploid set of chromosomes. The nucleotides in this reference are not necessarily the most frequent in the population. Therefore this reference genome is not a human genome, but just something to compare our reads with. It may contain haplotypes that do not exist in reality, because it's from multiple diploid individuals collapsed in a single haploid genome.

For a variant: the reference allele is the nucleotide of the reference genome at that position. An alternate allele is an allele not matching the reference allele. This may be the minor allele, but not necessarily because also the reference allele might be the minor allele.

[GK1610]

Thanks.. This is awesome!

[WouterDeCoster]

Happy to help. If an answer was helpful you should upvote it, if the answer resolved your question you should mark it as accepted.

Cheers, Wouter

[cpad0112]

Refer to G5, G5A, KG and KG-PROD tags in dbSNP (refer to dbSNP builds for hg19 equivalent NCBI genome) to know reference allele frequency. dbSNP includes allele frequency from 1000 genome and hapmap projects.

Answer 2

[Pierre Lindenbaum]

VCF specification: https://samtools.github.io/hts-specs/VCFv4.2.pdf

[GK1610]

Thanks but this document doesn't explain my questions.