User: sgalla32

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sgalla3230
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Posts by sgalla32

<prev • 3 results • page 1 of 1 • next >
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Answer: A: Why main diagonal of gemma relatedness matrix is not equal to 1
... The diagonals here remind me more of a kinship matrix (self-kinship = 0.5) than a relatedness matrix (self-relatedness = 1). I haven't used Gemma before, but other relatedness programmes (like the R-programme [KGD][1]) based on high-throughput sequencing data have given me self-relatedness values th ...
written 23 days ago by sgalla3230
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Comment: C: Using vcftools to filter SNPs by a linkage disequilibrium (r2) threshold
... Kia ora (thank you) Kevin! I just saw your other post here. It was very helpful! https://www.biostars.org/p/338289/ ...
written 4 weeks ago by sgalla3230
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Comment: C: Using vcftools to filter SNPs by a linkage disequilibrium (r2) threshold
... Hi everyone! I've got the same question and am wondering how you can actually prune for LD using VCFTools (not just identify the SNPs that are in LD). I'm wondering if you could use the command --hap-r2-positions to create a list of positions that are out of LD, and then use the --exclude-positions ...
written 4 weeks ago by sgalla3230

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