User: axelwilhelm

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axelwilhelm100
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100
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Location:
Sweden
Last seen:
4 years, 5 months ago
Joined:
6 years, 5 months ago
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Posts by axelwilhelm

<prev • 24 results • page 1 of 3 • next >
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Comment: C: Sorting with vcftools for tabix gone wrong
... This guy does (bo-peng). Damn tools written by others. ...
written 4.5 years ago by axelwilhelm100
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Comment: C: Sorting with vcftools for tabix gone wrong
... No, should I? ...
written 4.5 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 4.5 years ago by axelwilhelm100 • updated 10 months 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 4.5 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 4.5 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 4.5 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 4.5 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 4.5 years ago by axelwilhelm100 • updated 4.5 years ago by Matt Shirley8.9k
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Comment: C: PhD in bioinformatics or biostatistics as a wet-lab scientist?
... Are you implying that a man with a poor stature and an old weatherd face with grey hair and brown teeth is bad. I consider every man a larvae until they reach that point. And maybe he will have fun along the way in a far-off adventurous dimension. What he needs is a spouse that brings home the bacon ...
written 4.6 years ago by axelwilhelm100
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Comment: C: Problems installing samtools on linux (make command)
... Installing from command line did it. Command line is best. I do not know why I tried a browser download. I betrayed the command line, let it down and cheated on it. It punished me like the righteous all knowing, all powerfull higher being it is. That was my problem. Thank you for turning my straying ...
written 4.6 years ago by axelwilhelm100

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Popular Question 5.2 years ago, created a question with more than 1,000 views. For Viewing Multiple Regions In Samtools

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