Is there any R package for filtering out SNP markers?
1
0
Entering edit mode
prodhan82 ▴ 20
@prodhan82-21410
Last seen 2.5 years ago
Australia

Species: Oryza sativa Study: Identification of QTL for a particular trait I have a set of 3000 SNP markers across the rice genome. I want to reduce this set to 300 SNP markers. Queries: i. What are the criteria that I should apply to filter out the markers? ii. Are there any R packages to do it?

Thanks.

Tutorial annotation • 1.5k views
ADD COMMENT
1
Entering edit mode
prodhan82 ▴ 20
@prodhan82-21410
Last seen 2.5 years ago
Australia

I solved this issue using 'bcftools'. I wrote a quick tutorial in Biostars on how I did it. The link is here: https://www.biostars.org/p/423666/

ADD COMMENT

Login before adding your answer.

Traffic: 742 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6