How to extract mutation from...?
I have a VCF file in which the genome of the normal tissue is compared with that from the tumor in the same sample.
Using this VCF file, how can I get all of the mutations in this sample? (I'm using R 3.4.4)
Any idea & comment, even if they seem very basic to you highly appreciated.
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ruhollah •
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Is this a technical question like how to load a VCF into R? Please elaborate.
Probably not, most commonly both are compared to the reference genome for variant calling, not to each other.
If you take a look at the vcf specifications you'll see that alleles are encoded as 0 (ref) or 1 (alt). If you want to use R then that's something that you can filter on in a daraframe.
The OP is likely performing somatic variant calling, since they are talking about tumors and normals.
You previously clarified the concept: Somatic vs Germline Variant Calling
Isn't this VCF actually a text file of the differences (
mutationsif you want to call them that) you are looking for?