User: serpalma.v

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serpalma.v20
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Germany
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4 weeks ago
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Posts by serpalma.v

<prev • 73 results • page 1 of 8 • next >
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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 weeks 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 7 weeks ago by serpalma.v20 • updated 6 weeks ago by Kevin Blighe44k
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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 8 weeks 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 8 weeks 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 12 weeks ago by serpalma.v20 • updated 12 weeks ago by h.mon26k
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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 3 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 3 months ago by serpalma.v20
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Comment: C: Best tool for variant calling
... Hello! * Do you explicitly remove the duplicates? As far as I understand, if duplicates were marked, `mpileup` skips them. * If the flag `--min-MQ` is included, I guess step 2 is not necessary, right? ...
written 4 months ago by serpalma.v20
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Are both samtools mpileup options -m and -F only related to indel detection?
... Hello, I am a beginner in variant calling with `samtools` and trying to understand its usage. Often the options `-m` and `-F` are used, together with the option `-p`. This is what appears in the documentation for `samtools mpileup`: -p, --per-sample-mF apply -m and -F per-sample for incr ...
next-gen alignment samtools mpileup snp written 4 months ago by serpalma.v20
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Comment: C: How to select SNPs the most conservative way after WGS Variant Calling?
... Thanks Istvan OK, I will call variants with SAM/BCFtools on the same BAMs as well. Then I can subset both raw call sets by depth and allele frequency. Then consider common intersecting SNPs as the good ones. To filter by depth, I guess that I could only take the SNPs where all samples have a dept ...
written 4 months ago by serpalma.v20

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