User: spiral01

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spiral0170
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Posts by spiral01

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simulating slightly deleterious mutations in humans using a gamma distribution
... I am using SLiM to simulate slightly deleterious mutations in humans under a gamma distribution. From the literature I know that I can use a shape parameter of 0.23 and a mean parameter such that NeS=1000 (Eyre-Walker, Woolfit & Phelps, Genetics, 2006). However when Ne=100, this would leave a m ...
snp written 1 day ago by spiral0170
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Selscan error: Variant physical position must be strictly increasing.
... I am trying to use selscan to calculate EHH scores. I have 1000 genomes vcf files which I have used to produce map files with vcftools, such that they look like this: 22 rs8142737 50291889 50291889 22 rs570182536 50291936 50291936 22 rs8135816 50291976 50291976 22 rs8140681 50292081 ...
selscan map snp written 6 months ago by spiral0170
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Answer: A: vcflib GPAT++: How to select all individuals as targets?
... The argument requires a string as input. Therefore: sequence="$(seq -s ',' 0 2503)" echo $sequence produces the sequence as one long string of numbers. ...
written 6 months ago by spiral0170
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vcflib GPAT++: How to select all individuals as targets?
... I am attempting to run the iHS tool from the GPAT++ suite. It requires the target individuals to be listed as a zero based, comma separated list. I would like to apply this to all individuals in the 1000 genomes phase 3 vcf files. My command is: iHS --target <(seq -s ',' 0 2503) --file ../ch ...
vcf gpat++ vcflib snp written 6 months ago by spiral0170
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Comment: C: Set ancestral alleles to upper case in vcf file
... I have edited my question. Thanks. ...
written 7 months ago by spiral0170
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Set ancestral alleles to upper case in vcf file
... I am trying to set my reference allele as the ancestral allele in 1000genomes vcf files. I can do this using the `--derived` option in vcftools. However most of the ancestral alleles are in lowercase so vcftools is not able to correct for this. I am currently looking at a method of extracting the ...
snp written 7 months ago by spiral0170 • updated 7 months ago by Pierre Lindenbaum113k
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(Closed) Extract all genotype information for each individual in vcf file and store in separate files
... I would like to extract the genotypes for each individual in a vcf file and store them in separate files. So for instance, 1000 genomes vcf files have 2504 individuals. I would like to create 2504 files with the genotype at each position in a separate line. Is this possible? ...
vcf snp written 7 months ago by spiral0170
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Extract all genotype counts from phased data in vcf files
... I have vcf files (1000 genomes) with phased data and would like to extract counts of the genotypes. Several methods were suggested here: https://www.biostars.org/p/218444/ However, I need to extract not just the homozygous for ref, heterozygous, and homozygous for alt counts, but the counts for eve ...
vcf snp written 7 months ago by spiral0170 • updated 7 months ago by Pierre Lindenbaum113k
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Comment: C: Writing vcf file headers
... Thank you. Yes you can download the file from the link I sent above. Under resources you can download data. It is the vcf file for the AM population (I cannot link directly for some reason). ...
written 8 months ago by spiral0170
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Comment: C: Writing vcf file headers
... I didn't actually generate the file. It is from the pop fly drosophila database (http://popfly.uab.cat/). I confess that I am a primarily theoretical biologist and so do not generate my own data, so I am not particularly familiar with the vcf generation process. ...
written 8 months ago by spiral0170

Latest awards to spiral01

Popular Question 5 months ago, created a question with more than 1,000 views. For Phylogenetics in R: obtaining internal branch lengths
Great Question 6 months ago, created a question with more than 5,000 views. For Rooting phylogenetic trees in R using Ape's root function: Trees don't seem to root.
Scholar 6 months ago, created an answer that has been accepted. For A: Combining vcf files so that same loci data is combined
Supporter 10 months ago, voted at least 25 times.
Scholar 10 months ago, created an answer that has been accepted. For A: Combining vcf files so that same loci data is combined
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Rooting phylogenetic trees in R using Ape's root function: Trees don't seem to root.

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