Hello, I have a several samples analyzed with 50K beadchip. I want to extract a subset of 100 SNPs based on quality parameter and MAF, equally distributed by cromosome. Please there is some istruction to do it in Plink? Regards
First, filter per-chromosome/quality/maf with Plink. From there you can select how many SNPs from each per-chromosome filtered dataset to retain using the tool NGS: VCF Manipulation > VCFrandomSample or the tool Text Manipulation > Select random lines from a file (for the second, use a VCF without a header during line filtering, then add it back after if wanted). Merge the final results together using VCFcombine.
Hope this helps, Jen, Galaxy team