User: axelwilhelm

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axelwilhelm100
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Sweden
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1 week ago
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7 years, 11 months ago
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Posts by axelwilhelm

<prev • 26 results • page 1 of 3 • next >
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Comment: C: Tools to calculate binned Dxy?
... Here is the answer [https://www.biostars.org/p/430249/#460863][1] [1]: https://www.biostars.org/p/430249/#460863 ...
written 10 days ago by axelwilhelm100
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Answer: A: Sliding window analysis for angsd output
... Matteo Fumagalli has this tutorial [https://github.com/mfumagalli/ngsTools/blob/master/TUTORIAL.md][1] [1]: https://github.com/mfumagalli/ngsTools/blob/master/TUTORIAL.md It has a section about nucleotide diversity with sliding window R scripts ...
written 10 days ago by axelwilhelm100
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Comment: C: Sorting with vcftools for tabix gone wrong
... This guy does (bo-peng). Damn tools written by others. ...
written 6.0 years ago by axelwilhelm100
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Comment: C: Sorting with vcftools for tabix gone wrong
... No, should I? ...
written 6.0 years ago by axelwilhelm100
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Sorting with vcftools for tabix gone wrong
... I concatenated two vcf files by scripting, keeping only the header from the first file and adding an extra column in the end to know which file each line is coming from. I do this: tabix -p vcf f1PotMut.vcf.gz and get this: [ti_index_core] the chromosome blocks not continuous at line 87352, is ...
vcf tabix sort vcftools index written 6.0 years ago by axelwilhelm100 • updated 2.4 years ago by Biostar ♦♦ 20
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Answer: A: To remove genotype "./." from vcf file with awk
... something like awk 'substr($10,0,3)!="./.", substr($11,0,3)!="./.", substr($12,0,3)!="./.", substr($13,0,3)!="./."' ...
written 6.0 years ago by axelwilhelm100
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Comment: C: No vcf output from vcftools
... I did, back and forth, missed the obvious and posted here. Sometimes people get dyslexic for what they are searching for. Like having the glasses on the eyebrows while searching for them. ...
written 6.0 years ago by axelwilhelm100
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No vcf output from vcftools
... I thought this command would give me a new vcf file without the individuals in the text file: `vcftools --gzvcf mergedPF.vcf.gz --remove listPnsToRemoveFromMergedVcf.txt --out filtMergedPTrios` Instead it gives me an index file and a log file. I must be missing some obvious point. I want to filte ...
vcf remove vcftools written 6.0 years ago by axelwilhelm100
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Comment: C: Do file extensions effect files
... It is binary data so its no use posting heads. ...
written 6.0 years ago by axelwilhelm100
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Do file extensions effect files
... I just created a bed file from the GATK walker VariantsToBinaryPed. It was of course supposed to be a ped file. Now I can't use it as input to phaseByTransmission. My question is: is the file crap even if I change the file ending afterwards? If so, are all filetypes so sensitive?   And while I'm a ...
gatk file extension unix ped linux written 6.0 years ago by axelwilhelm100 • updated 6.0 years ago by Matt Shirley9.4k

Latest awards to axelwilhelm

Great Question 5.9 years ago, created a question with more than 5,000 views. For Sorting with vcftools for tabix gone wrong
Great Question 5.9 years ago, created a question with more than 5,000 views. For Problems installing samtools on linux (make command)
Epic Question 5.9 years ago, created a question with more than 10,000 views. For Problems installing samtools on linux (make command)
Popular Question 5.9 years ago, created a question with more than 1,000 views. For Do file extensions effect files
Popular Question 5.9 years ago, created a question with more than 1,000 views. For Heterochromatic Region Dyz19
Popular Question 5.9 years ago, created a question with more than 1,000 views. For Gene/Protein Name Etymology
Popular Question 5.9 years ago, created a question with more than 1,000 views. For Samtools Pileup Characters
Popular Question 5.9 years ago, created a question with more than 1,000 views. For No vcf output from vcftools
Popular Question 5.9 years ago, created a question with more than 1,000 views. For Samtools: Why Have I Been Using "View" Command For Mpileup
Popular Question 5.9 years ago, created a question with more than 1,000 views. For Sorting with vcftools for tabix gone wrong
Popular Question 5.9 years ago, created a question with more than 1,000 views. For Viewing Multiple Regions In Samtools
Popular Question 6.7 years ago, created a question with more than 1,000 views. For Viewing Multiple Regions In Samtools

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