Questions tagged [variant]

The tag has no usage guidance.

Filter by
Sorted by
Tagged with
19
votes
4answers
4k views

Do all humans have an identical nucleotide sequence for certain proteins, e.g haemoglobin?

All humans have the same sort of proteins in our bodies. Take haemoglobin for example. Is the gene coding for haemoglobin in my body identical to everyone else's gene or is there slight variations ...
2
votes
3answers
274 views

What is a sequencing artifact?

I'm rather new to bioinformatics, so this might be a rather basic question, but what are sequencing artifacts, in the context of variant calling?
0
votes
3answers
56 views

why and how multi allele gets reported during variant calling in vcf?

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 ...
1
vote
0answers
30 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
vote
3answers
250 views

How to get phased haplotype from vcf file?

Although I'm reading all days and nights, still confused in this area. I have hundreds of BAM files (from whole-genome sequencing of a given human population). I was wondering how I can obtain phased ...
2
votes
3answers
255 views

Definition of the different DNA regions

Reading from Oshima et al. (2016): We identified 3,868 noncoding mutations including 394 located <5 Kb downstream, 1,762 intergenic, 1,621 intronic, 81 <5 Kb upstream, 7 UTR 3′, 2 UTR 5′, and ...
2
votes
1answer
64 views

What is this passage trying to say about Darwin's difficulty in explaining variation?

This passage, from the book "How humans evolved" by Robert Boyd, says that one of the problems Darwin had at the time was that he struggled to convincingly explain how variation could be maintained; ...
3
votes
3answers
76 views

Online resource for downloading gene variant data?

I have a long list of gene variations. For example, Here are 4 of them: CBL Q249E TERT H412Y SF3B1 R625H EGFR L747_T751delinsP The first term identifies the gene, the second identifies the ...
1
vote
0answers
31 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 ...
2
votes
0answers
61 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 ...
1
vote
0answers
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 ...
3
votes
0answers
93 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): ...
6
votes
1answer
761 views

Are four-leaf clovers mutations, developmental errors, or something more complicated?

What causes about 1 in 10,000 clovers to have four instead of three leaves? Will progeny(?) grown from its flower's seeds have a higher probability than that of also having four leaves? From the ...
1
vote
1answer
324 views

Does zygosity have meaning for mitochondrial variants?

I am working on a system that annotates variants in human DNA sequences. One of the pieces of information reported is the zygosity of the variant. I noticed that mitochondrial variants are also shown ...
0
votes
1answer
1k views

Variant VCF: AD vs DP?

In my VCF file from GATK, I have the following definitions for AD and DP. ...