Entering edit mode
8.6 years ago
biogeek
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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!
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:
At the end, there are no definite/default values for variant significance.