User: lovestowell

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lovestowell10
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Posts by lovestowell

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Comment: C: strange He vs Fst plot from Lositan
... Hi, I never did get a satisfactory answer to this question. I ended up concluding that it was a problem with the particular genome of my species and how it was sequenced (a salmonid with an ancient whole genome duplication, leading to an overrepresentation of many sequences in a MiSeq run) as well ...
written 2.5 years ago by lovestowell10
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Allocation error from PolyRelatedness
... Anyone out there using PolyRelatedness? I have 1000s of SNPs from 16 individuals and I would like to calculate pairwise relatedness. I'm looking for a relatedness estimator that allows for both polyploidy and inbreeding. When I run PolyRelatedness I get an error and I'm not sure what's causing it. A ...
relatedness polyrelatedness polyploidy snp written 3.3 years ago by lovestowell10
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Find particular SNPs affecting PCA
... Hey there, I have a set of ~13K SNPs across 16 individuals, 8 from each of two different species. Individuals were sequenced in two different sequencing runs. I am using the R package SNPRelate to calculate relatedness between pairs and to visualize the individuals in PCA space. The problem is that ...
myposts pca snp snprelate written 3.4 years ago by lovestowell10 • updated 3.4 years ago by mkulecka300
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strange He vs Fst plot from Lositan
... I'm working with a panel of 13K SNPs generated using a modified ddRAD library prep. The two "populations" are survivors vs dead of the same inbred individuals. I'm trying to use Lositan to test for outlier loci between these two groups but as you can see below, I'm getting a crazy plot for He vs Fst ...
he myposts fst snp lositan written 3.5 years ago by lovestowell10
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Answer: A: file formatting for SNPRelate
... In case anyone else is having the same problem and also didn't read the man pages carefully... Both snpgdsVCF2GDS() and snpgdsIBDMLE() have some extra arguments that make things work more smoothly. I wasn't sure if the sex chromosome in my original VCF file was part of the trouble, so I removed it ...
written 3.6 years ago by lovestowell10
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file formatting for SNPRelate
... Hello! I am trying to use the R package SNPRelate to calculate pairwise relatedness between 8 males and 8 females. I have a VCF file with ~13,000 SNPs. I am able to use SNPRelate to convert the VCF file to a GDS file with snpgdsVCF2GDS(). However, when I try to use the functions that act on the GDS ...
vcf file fomat relatedness gds snprelate written 3.6 years ago by lovestowell10
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Comment: A: convert list of positions to BED file
... Thanks! That's a great start, but that still gives me runs of only a single base, like so... chrUn 1 2 chrUn 2 3 chrUn 3 4 ... when what I need is something like this... chrUn 1 512 chrUn 598 733 chrUn 852 1229 ... I think I need some sort of conditional statement, where if $2-1 = 1, then ...
written 4.0 years ago by lovestowell10
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convert list of positions to BED file
... Hello, I'm trying to use samtools mpileup to generate a SNP table from individual samples aligned to a reference genome. I want to use the -l flag so that only certain positions in the reference are used to call the SNPS.  Here's what I'm trying: samtools mpileup -g -b ~/Data/alignments/bamfilena ...
samtools mpileup bed file list of positions written 4.0 years ago by lovestowell10

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