phased data for plink2 alpha

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Akhil Pampana

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Oct 7, 2019, 4:19:47 PM10/7/19
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can plink handle phased data? I see in documentation that it can handle in latest version but i am not getting variants list when i am doing ldprunning on phased genotypes vcf. Can you help me out? 
command:`plink2 --pfile Black.freeze.8.total.filtered -maf 0.01 --indep-pairwise 50 5 0.2 --out LDpruned`

Christopher Chang

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Oct 7, 2019, 4:36:37 PM10/7/19
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This type of question is more appropriate for the plink2-users group.  But yes, plink2 shouldn't have a problem here (though --indep-pairwise does not take the phasing into account).  Can you post the problematic .log file in plink2-users?
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