How to extract mutation from...?

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6.0 years ago

ruhollah ▴ 10

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.

Cancer genome • 1.7k views

ADD COMMENT • link 6.0 years ago by ruhollah ▴ 10

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Is this a technical question like how to load a VCF into R? Please elaborate.

ADD REPLY • link 6.0 years ago by ATpoint 82k

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I have a VCF file in which the genome of the normal tissue is compared with that from the tumor

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.

ADD REPLY • link 6.0 years ago by WouterDeCoster 47k

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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

ADD REPLY • link 6.0 years ago by igor 13k

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Isn't this VCF actually a text file of the differences (mutations if you want to call them that) you are looking for?

ADD REPLY • link 6.0 years ago by GenoMax 142k

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