User: serpalma.v

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serpalma.v20
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New User
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Germany
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1 day, 15 hours ago
Joined:
5 years, 11 months ago
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Posts by serpalma.v

<prev • 76 results • page 1 of 8 • next >
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How to replicate vcftool's sliding window SNP density?
... Hello! vcftools can calculate statistics such as pi and Fst using sliding windows. I've noticed that windows in which the alternative allele is fixed are not taken into account. However, those appear in the VCF file. For example, ``N_VARIANTS`` for pi at window_x is 20, but the region in the vcf ...
vcftools snp sequencing written 5 weeks ago by serpalma.v20 • updated 4 weeks ago by Vitis2.2k
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Comment: C: How does plink calculates linkage disequilibrium (r2) in unphased data?
... Would the result have the same interpretation as `r^2=D^2/(p1p2q1q2)`? ...
written 7 weeks ago by serpalma.v20
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How does plink calculates linkage disequilibrium (r2) in unphased data?
... Hello when I pass a vcf file to plink, it can calculate the linkage disequilibrium (r2) even though the data is not phased. How is this possible when the haplotype frequencies for SNP pairs are not known? Thanks! ...
plink snp sequencing written 7 weeks ago by serpalma.v20 • updated 7 weeks ago by chrchang5235.6k
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Comment: C: Interpretation of full LD between extremely distant SNPs
... Thank you for the input I went through the steps I applied to the data and it seems to be in order. I was suggested to make sure that all sites that were not-polymorphic were removed (all samples 0/0 or 1/1), but the picture remains almost the same. Previously I did PCA, ADMIXTURE, and hierarchic ...
written 5 months ago by serpalma.v20
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Interpretation of full LD between extremely distant SNPs
... Hello I evaluated the genome-wide LD decay by using snps separated by at least 10Kb using 'popLDdecay'. In the figure, each dot represents the mean r^2 of all pairs of snps that are separated at a given distance. The maximum distance corresponds to the length of the longest chromosome. The tren ...
linkage disequilibrium snp written 5 months ago by serpalma.v20 • updated 5 months ago by Kevin Blighe49k
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How to set the size of window for calculating Fst?
... Hello, I am trying to determine the window size to calculate Fst between two populations at each SNP within, then get the average of those Fst's. Do this in a sliding window approach. I've seen a [study][1] stating that the size of the window was determined by estimating the length of linkage diseq ...
window fst snp written 5 months ago by serpalma.v20
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Scanning for selection using rehh2 from mouse WGS VCF
... Hello I am trying to impletement `rehh2` to identify signatures of selection with ``iHS``. I have a vcf file, fresh out of the ``gatk`` pipeline and I see it needs to be phased. I intend to do this with ``shapeit2`` which requires a genetic map. Once the phased haplotypes are ready, I should be ...
mouse rehh2 sequencing written 5 months ago by serpalma.v20
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How to detect outliers from either (a) SNP-Fst or (b) Window-Fst distributions?
... Hello I want to find the SNPs that could be responsible for the phenotype differences observed between three populations. For that I computed Fst (weir and cockerham) using ``vcftools``. One population reflects the founder population (line0) from which the two populations were selected (line1 and ...
fst vcftools written 6 months ago by serpalma.v20 • updated 6 months ago by h.mon27k
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Comment: C: Best tool for variant calling
... Thanks again! just one more question to understand `--per-sample-mF`. I read that `m` corresponds to the min number of gapped reads for indel candidates (default: 1) and `F` corresponds to the min fraction of gapped reads (default: 0.002). Does this mean that `--per-sample-mF` is applicable only ...
written 7 months ago by serpalma.v20
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Comment: C: Best tool for variant calling
... Thanks! do you filter secondary and supplementary alignments? or are those assumed to be removed by filtering by mapping quality? ...
written 7 months ago by serpalma.v20

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