Question: why and how multi allele gets reported during variant calling in vcf
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gravatar for genie66
6 months ago by
genie6620
United States
genie6620 wrote:

This might be a very basic question for many here. With the basic understanding of inheritance, eventhough there is a possibility of multiple genotypes due to multi alleles, the resulting genotype can only have two alleles(paternal and maternal) that way after variant calling, an allele at one position can be homozygous or heterozygous. So there can be max of two alleles, but why do we see multiple alleles at a given position in single sample VCF. I am trying to understand the science behind this. Please help out. Thanks!

Eg:

chr5    127640782   .   AG  A,AA    .   .   .   GT:AD:DP    1/2:0,28,409:437
ADD COMMENTlink modified 6 months ago • written 6 months ago by genie6620

the resulting genotype can only have two alleles(paternal and maternal)

for one sample, yes. If there is more than one sample in the VCF for the same variant: sample 1 is A/T, sample2 is T/G ...

ADD REPLYlink written 6 months ago by Pierre Lindenbaum119k
1

To add to what Pierre said, even in situations where there is a single sample, multi-alleles appear due to the fact that NGS data has such high error rates. It is difficult for the in silico tools to deal with this messy data in a way that is faithful.

Indels should dominate the multi-allelic regions, too, as indels are inherently difficult to call for a variant caller.

ADD REPLYlink written 6 months ago by Kevin Blighe41k

Please don't ask the same question on multiple boards at the same time. If you already have a good answer on one board, it's a waste of people time to repeat it here.

ADD REPLYlink written 6 months ago by swbarnes25.3k

Some times, both maternal and paternal are alternate alleles if reference is not exact reference.

ADD REPLYlink written 6 months ago by cpad011211k
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