How to count variant frequencies in set of vcf lists

Question

[sanna.gudmundsson]

Hi,

I have exome sequencing data from about 50 individuals. I would like to generate the frequencies of each variant in my dataset. Do you have any suggestions for easy to use tools from e.g. samtools or GATK?

What I want to be able to do in the end is filter out things that are present in my "in-house data base" to get rid of sequencing artefacts.

Thanks in advance!

Sanna

[Pierre Lindenbaum]

I have exome sequencing data from about 50 individuals.

50 vcf files with 1 sample

or

1 vcf file with 50 samples ?

I would like to generate the frequencies

if it's one file, then those frequences should already be available in the INFO/AF attribute...

[sanna.gudmundsson]

Sorry I think Im not being clear.

I have 50 vcf files (whole exom) for 50 individuals. I would like to filter my data towards the 50 files.

I want to know how many times in my 50 files a certain variant occurs. For example, maybe generate a master vcf with all variants found in my 50 individuals and an informative string of how often they occur as heterozygous AF=0/1 or homo 1/1.

Is there a simple tool that you know of that does this? samtools, bcftools or similar?

Sanna