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Question: extract a SNPs set based on polimorfism in Plink
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gravatar for landivincenzo
15 months ago by
landivincenzo • 0
landivincenzo • 0 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
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modified 15 months ago by Jennifer Hillman Jackson ♦ 25k • written 15 months ago by landivincenzo • 0
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gravatar for Jennifer Hillman Jackson
15 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

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 COMMENT • link written 15 months ago by Jennifer Hillman Jackson ♦ 25k

Thank you very much Jennifer!

ADD REPLY • link written 14 months ago by landivincenzo • 0
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