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Selecting variants from a VCF file

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

variant snp vcf next-gen
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updated by Ram Ram • written by matt.christmas85 • matt.christmas85

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

Thanks

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written by panatheod • panatheod

1 answer

"SnpSift filter" is quite powerful

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updated by Ram Ram • written by Pablo Pablo

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