Question: extract a SNPs set based on polimorfism in Plink
gravatar for landivincenzo
9 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 • 264 views
ADD COMMENTlink modified 8 months ago by Jennifer Hillman Jackson25k • written 9 months ago by landivincenzo0
gravatar for Jennifer Hillman Jackson
8 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 8 months ago by Jennifer Hillman Jackson25k

Thank you very much Jennifer!

ADD REPLYlink written 8 months ago by landivincenzo0
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 81 users visited in the last hour