User: spiral01

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spiral0170
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Posts by spiral01

<prev • 84 results • page 1 of 9 • next >
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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 3 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 3 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 3 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 4 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 4 months ago by spiral0170 • updated 4 months ago by Pierre Lindenbaum110k
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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 4 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 4 months ago by spiral0170 • updated 4 months ago by Pierre Lindenbaum110k
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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 5 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 5 months ago by spiral0170
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Comment: C: Writing vcf file headers
... Thanks. I have edited to include both the header and the first few lines. ...
written 5 months ago by spiral0170

Latest awards to spiral01

Great Question 3 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 3 months ago, created an answer that has been accepted. For A: Combining vcf files so that same loci data is combined
Supporter 7 months ago, voted at least 25 times.
Scholar 7 months ago, created an answer that has been accepted. For A: Combining vcf files so that same loci data is combined
Popular Question 22 months 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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