Interpreting data from caveman vcf file - when is a mutation significant?
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7.0 years ago
biogeek • 0

There is a very nice description in the beginning of the vcf file saying:

Can anyone elaborate a little bit on the MP, GP, TG, TP, SG and SP information? And what does it mean when my first example is like this:

How do I decide if this mutation is actually significant or not? As far as I can see, the proportion of mutated alleles are 12% - but is that enough to say that the cell line will be mutated at the specific position? And is there any kind of p-value describing how significant the mutation is?

Thank you so much in advance!

gene vcf SNP sequencing mutation • 2.2k views
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Refer to the VCF format description and software documentation

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Okay

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I have a following question:

I looked at the hg18,hg19 and hg38 for chr1:130 position (as mentioned above). Reference base is not found in any of these references. Is this human genome?

My best guess is that (as inferred from VCF description), EM guesses possible Genotypes and gives out their probabilities. Genotype with highest probability would be considered/used for alternate allele inclusion in VCF.

In my opinion, there are two kinds of significance for a variant:

  1. Mapping significance: Quality values generated till variant calling (Informatics tier 1 as per HL-7 CG template): Multiple probability values generated till variant calling: e.g., BQ, MQ and other values such as Homopolymer Run, Read depth etc
  2. Functional significance: Significance that comes from functional annotation: e.g., Nonsynonymous (missense and nonsense), NMD, splice site alteration, pathogenic etc etc. It also depends context of variant analyzed (e.g., end point)

At the end, there are no definite/default values for variant significance.

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