Selecting variants from a VCF file

Question

[matt.christmas85]

I have generated a VCF file as an output from the GATK UnifiedGenotyper. However, I have quite a lot of missing data in my data set. Does anyone know a way of selecting SNPs that are, say, represented by at least 80% of my samples and therefore excluding any that are below this?

Also, I have multiple SNPs per contig, I would like to get a set of SNPs where there is only one per contig to reduce the effects of linkage. Does anyone know a way of randomly selecting one SNP per contig or, for example, selecting the SNP with best coverage/quality score per contig to leave me with a dataset where each SNP is from a separate contig?

Thanks

[Pierre Lindenbaum]

see Reliable Tools To Filter Vcf Format Files

[matt.christmas85]

Thanks Pierre

[panatheod]

Sorry but I am curious did you finally found a way to randomly sample one snp per ID (contig) from a vcf file?

Thanks

Answer 1

[Pablo]

"SnpSift filter" is quite powerful