User: outlier95
outlier95 • 10
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Posts by outlier95
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... Thanks! Very helpful information. ...
written 2.4 years ago by
outlier95 • 10
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... I simply want to compare genetic divergence between two populations using two different marker types, microsatellites and snps. What would be a suggested approach? I realize there are probably several ways to go about this, but any general idea would be great. Thanks. ...
written 2.4 years ago by
outlier95 • 10
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... For analysis of Fst with microsatellite loci, is it appropriate to use the Weir and Cockerham estimator of Fst as opposed to other estimators? I've seen mixed use in the literature. ...
written 2.5 years ago by
outlier95 • 10
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... I see that now :). I will try and report back if I have any issues. Thanks again... ...
written 2.7 years ago by
outlier95 • 10
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... Could you please provide a simple example using vcf-contrast or vcf-isec to get me started? Thanks. ...
written 2.7 years ago by
outlier95 • 10
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... If I remove singletons and private doubletons via --singletons and --positions using VCFtools, then take the difference in the number of SNPs before and after filtering, should that amount to the number of informative SNPs (per my definition)? Many thanks. ...
written 2.7 years ago by
outlier95 • 10
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... MOD-EDIT: OP has opened a new question for this here: https://www.biostars.org/p/196499/ ...
written 2.7 years ago by
outlier95 • 10
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... I want to identify private and shared polymorphisms between two .vcf files (or multi-sample vcf) using VCFtools. Any suggestions would be great. Thanks.
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written 2.7 years ago by
outlier95 • 10
• updated
6 months ago by
Jorge Amigo ♦ 11k
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... Wondering how I can get the number of informative sites in a .vcf file using VCFtools. By informative I mean at least two samples share a variant. Any suggestions? Thanks. ...
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... Well the contig lengths in the vcf swbarnes2 is referring to are all the reference contigs, regardless if reads supported a given contig (at least in my vcf file). I just want the lengths of all the contigs from the CHROM column. ...
written 2.7 years ago by
outlier95 • 10
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