Questions tagged [variant]

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6 questions with no upvoted or accepted answers
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76 views

Is a novel homozygous SNV reasonable?

I'm doing some variant discovery in a human trio (affected child, non-affected mother, non-affected father) and I have found what looks like a homozygous novel mutation. All of the aligned reads in ...
3
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0answers
109 views

Use of pipe character in VCF info field

While annotating my VCF file with ClinVar, I noted the following value for the CLNSIG field (i.e., clinical significance): ...
1
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0answers
31 views

The concept of high genetic load of disease and non-random segregation of deleterious variants

I'm new in this field. I was reading Shakeel et al. (2018) and came across the below sentences The rate of emergence and distribution of deleterious variants in populations is important in ...
1
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0answers
33 views

What are the exact reason causing missing calls in a VCF file from exome sequencing?

My data is a VCF file from exome sequencing variant call. I'm not very familiar with the sequencing process and variant calling process. I noticed that there are some missing genotypes, which is ...
1
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38 views

Are VCF headers supposed to change over time?

VCF headers describing the content of the INFO field are supposed to give additional information about a variant. Example. A VCF file can be annotated against ...
0
votes
0answers
28 views

What does an allele frequency of 0 mean in gnomAD v3?

There is a single nucleotide variant: 18-47394-G-A (GRCh38) with an allele count and allele frequency of 0. As I understand it, this means that there are no alleles in the population with this variant,...