User: axelwilhelm
axelwilhelm • 100
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Posts by axelwilhelm
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... Trying to open Beast with a nexus file and get this:
> [Fatal Error] :1:1: Content is not allowed in prolog.
Maybe Beast does not like the nexus format
Maybe I have to convert my file to XML
By the way, I have never been able to open anything in Beast so it might be a bigger problem
Using BE ...
written 3 months ago by
axelwilhelm • 100
• updated
8 weeks ago by
Biostar ♦♦ 20
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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 4 months ago by
axelwilhelm • 100
0
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... 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 4 months ago by
axelwilhelm • 100
1
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5.4k
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... This guy does (bo-peng). Damn tools written by others.
...
written 6.3 years ago by
axelwilhelm • 100
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... No, should I?
...
written 6.3 years ago by
axelwilhelm • 100
4
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1
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5.4k
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... 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 ...
written 6.3 years ago by
axelwilhelm • 100
• updated
2.7 years ago by
Biostar ♦♦ 20
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2
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... something like
awk 'substr($10,0,3)!="./.", substr($11,0,3)!="./.", substr($12,0,3)!="./.", substr($13,0,3)!="./."'
...
written 6.3 years ago by
axelwilhelm • 100
1
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1
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4.2k
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1
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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 6.4 years ago by
axelwilhelm • 100
4
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... 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 ...
written 6.4 years ago by
axelwilhelm • 100
1
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3
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1.5k
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3
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Comment:
C: Do file extensions effect files
... It is binary data so its no use posting heads.
...
written 6.4 years ago by
axelwilhelm • 100
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