filtering out rsid from vcf files.

Question

[rheab1230]

Hello, I have a vcf file in which there are many snp matching to genes. So one gene have many rsid values to it. I want to filter the vcf file so that it contain only 100 rsid uniquely mapped to 100 genes. meaning each gene should matched to only 1 SNP and not many. I tried to use bcftools filter option but not getting desired results. This is how my one rsid value in vcf file look like;

22      16050075        rs587697622     A       G       100.0   PASS    AC=1;AF=0.000199681;AN=5008;NS=2504;DP=8012;EAS_AF=0;AMR_AF=0;AFR_AF=0;EUR_AF=0;SAS_A
F=0.001;AA=.|||;VT=SNP;ANN=G|intergenic_region|MODIFIER|CHR_START-LA16c-4G1.3|CHR_START-ENSG00000233866|intergenic_region|CHR_START-ENSG00000233866|||n.16050
075A>G||||||  GT  

So this rs587697622 corresponds to ENSG00000233866 but there are several rsid corresponding to this gene. I just want to filter unique rsid mapped to one gene only.

[rheab1230]

I am trying to create a simulated data using only one snp mapped to one gene id. I can use multiple variations for the gene but it will take a lot of time. So I taught of taking only unique rsid mapping to just unique genes and consider those for my simulated studies.

[Istvan Albert]

this is one of those problems that pretty that very few people needed to solve before, hence a ready-made solution may not available,

but at the same time is one that is almost trivial to solve with minimal programming skills:

read the file, collect the gene names, then output a line only if the gene has not been seen before, just a few lines of code really