Question: extract a SNPs set based on polimorfism in Plink
gravatar for landivincenzo
15 months ago by
landivincenzo0 wrote:

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

snp plink • 534 views
ADD COMMENTlink modified 15 months ago by Jennifer Hillman Jackson25k • written 15 months ago by landivincenzo0
gravatar for Jennifer Hillman Jackson
15 months ago by
United States
Jennifer Hillman Jackson25k wrote:


The Plink tool wrapped for Galaxy could be installed and used in a local, docker or cloud Galaxy for most of the filtering.

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

ADD COMMENTlink written 15 months ago by Jennifer Hillman Jackson25k

Thank you very much Jennifer!

ADD REPLYlink written 14 months ago by landivincenzo0
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