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Linkage Disequilibrium Analysis

MR Marta Rusmini
PU Paolo Uva
AA Antonio Amoroso
MT Manlio Tolomeo
AC Andrea Cavalli
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Haploview (26) was used to identify variants in Linkage Disequilibium (LD). First, variants in VCF format were converted by vcftools (27) in the input format required by Haploview (26). Only common variants, significantly correlated with COVID19 cases, selected as described above and considered divided for chromosomes, were retained for Haploview analysis, using default parameters. Furthermore, an application of Haploview, named Tagger (28), has been used on all the single nucleotide variants (SNVs) to identify tag SNVs, i.e. SNVs which are representative of a group of SNVs in LD.

Copyright and License information:  ©2021 Rusmini, Uva, Amoroso, Tolomeo and Cavalli.
This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

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