Question

Linkage disequilibrium with one sample

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4.3 years ago

felipead66 ▴ 110

I have vcf files for various cultivars. Can I calculate linkage disequilibrium from a vcf file of only one cultivar or should I group them somehow?

ld plink19 • 777 views

ADD COMMENT • link updated 4.3 years ago by chrchang523 10k • written 4.3 years ago by felipead66 ▴ 110

score 2 · Answer 1 · 2020-01-03

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4.3 years ago

chrchang523 10k

Linkage disequilibrium computations require population data. The latest PLINK 2.0 build errors out if you attempt them with less than 50 samples.

ADD COMMENT • link 4.3 years ago by chrchang523 10k

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I thought so. Thank you very much for your answer.

ADD REPLY • link 4.3 years ago by felipead66 ▴ 110