User: outlier95

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outlier9510
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Posts by outlier95

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Comment: C: comparison of divergence between different markers
... Thanks! Very helpful information. ...
written 2.9 years ago by outlier9510
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comparison of divergence with different markers
... 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. ...
snps microsatellites written 2.9 years ago by outlier9510
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Fst (Weir and Cockerham estimator)
... 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. ...
microsatellites fst populuation genetics written 2.9 years ago by outlier9510
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Comment: C: Identifying private and shared SNPs using VCFtools
... I see that now :). I will try and report back if I have any issues. Thanks again... ...
written 3.1 years ago by outlier9510
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Comment: C: Identifying private and shared SNPs using VCFtools
... Could you please provide a simple example using vcf-contrast or vcf-isec to get me started? Thanks. ...
written 3.1 years ago by outlier9510
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Comment: C: Filtering on the minor allele in VCFtools
... 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 3.1 years ago by outlier9510
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Comment: C: Filtering on the minor allele in VCFtools
... MOD-EDIT: OP has opened a new question for this here: https://www.biostars.org/p/196499/ ...
written 3.1 years ago by outlier9510
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Identifying private and shared SNPs using VCFtools
... I want to identify private and shared polymorphisms between two .vcf files (or multi-sample vcf) using VCFtools. Any suggestions would be great. Thanks. ...
snps vcftools written 3.1 years ago by outlier9510 • updated 11 months ago by Jorge Amigo11k
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Filtering on the minor allele in VCFtools
... 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. ...
snps vcftools written 3.1 years ago by outlier9510 • updated 3.1 years ago by Adam990
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Comment: C: getting chromosome lengths from a vcf file
... 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 3.1 years ago by outlier9510

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