Filter only SNPs in 1000 Genomes Data Slicer

Question

[irieljoerin]

Hi all, I´m trying to retrieve genotypic data from 70 SNPs (from different chromosomes) from certain 1000 Genomes populations. I plan to use Data Slicer to create vcf for each variant and then merge them all in R with VariantAnnotation package. However, when I create the vcf in Data Slicer structural variants come together, and I just want to retrieve SNPs. Is there any strategy to retrieve only SNP data? Or, Can anybody suggest a different strategy to do this? I need that data to perform a structure/admixture analysis. Thanks in advance!

Answer 1

[harold.smith.tarheel]

It's probably easiest to filter the VCFs after retrieval. VCFtools --remove-indels or vcflib vcfsnps will do the job.