how to filter snps for specifice genes

Question

[forever]

I have ped file and I need to filter snps which only belong to Alzheimer genes?

[Medhat]

you can use SnpSift with annotated vcf file (Convert plink files to VCF: Reference allele file )

java -jar SnpSift.jar filter " (ANN[*].GENE = 'Alzheimer genes')" ann.vcf >result.vcf

Alzheimer genes = your gene of interest

Answer 1

[forever]

I have BED, BIM, FAM and PED files. I need only the genotypes of genes belong to Alzheimer?