How can I set a feature based on a single mutation in specific location?

Question

[morovatunc]

Hi,

I have more than ~2500 patients and all of them have mutation calling files. (VCF). I would like to subset my patients based on the occurrence of a specific location.

I have thought about giving the location of the mutation as a bed file and filter patients based on that(with snpsift or vcftools). But is there a known method to do this task and get TRUE/FALSE output ?

Best regards,

Tunc.

[WouterDeCoster]

You mean you have 2500 separate vcf files? Why not merge those together to one vcf?

[morovatunc]

Thank you for your reply. I keep the data in a single data frame such as TRUE or FALSE so it would be better get information for every individual.

in ex:

PatientA True
PatienB False
PatienC True

[WouterDeCoster]

I don't get it. Why not create one multisample vcf?

[morovatunc]

How can I obtain the information of which patient has that specific mutation if I merge all of my vcfs in to the same one unionvcf ?

I only would like to get information such as if a single mutation is existed.

[WouterDeCoster]

You will get a vcf in which every patient will have his own info field, containing genotype, quality and depth information.

[morovatunc]

I couldnt understand the part where we test the occurrence of the mutation. Could you prefer me a tool for that ?

Best,

Tunc.

[WouterDeCoster]

You can probably get this done using vcfmerge from vcftools or gatk combinevariants