User: Chico Fernandez

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3 years, 5 months ago
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Posts by Chico Fernandez

<prev • 25 results • page 1 of 3 • next >
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Comment: C: Filtering of low coverage variants from VCF
... Thank you...the problem is that I do not know the threshold that I want =( also I have a huge amount of data and would like to filter variants on-line (so do not even put unreliable results to the resulting vcf file after first GATK lunch)...I know that I want too much, but it would save a lot of me ...
written 3.6 years ago by Chico Fernandez70
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Comment: C: Filtering of low coverage variants from VCF
... Thank you...what threshold would you recommend for average coverage 30x? Which of the parameters are most important? As a mathematician, I would use only QUAL (likelihood) as a measure, even without depth, but is it OK? ...
written 3.6 years ago by Chico Fernandez70
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Comment: C: Filtering of low coverage variants from VCF
... Yes, thanks, but that's not what I want to do. I would like to find a strategy for removal of low-quality variants, depth of coverage seems too rough to be really efficient. For example, coverage 40 to ref allele and 5 to alternative will pass this filter, but together with low quality of bases of a ...
written 3.6 years ago by Chico Fernandez70
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Filtering of low coverage variants from VCF
... I would like to use GATK to obtain the distribution of variants, but I have some calls with low support, for example, I do not trust a call that tells me that it was founded in 2 reads. I can use simple coverage-based filter (say, depth for more than 20 bases is good and less is bad), but I am sure ...
vcf filtering written 3.6 years ago by Chico Fernandez70 • updated 3.6 years ago by harold.smith.tarheel4.4k
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Comment: C: Coordinates of centromers in human chromosomes
... But it is a clear duplicate. I was working 12 hours in a row and did not notice "head" inside the bash command. This question will not help anybody else, so do not know why not to close it. But you're the boss. ...
written 3.7 years ago by Chico Fernandez70
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Comment: C: Coordinates of centromers in human chromosomes
... Hello Chico Fernandez! Questions similar to yours can already be found at: How Can I Get The Human Chromosome Centromere Position And Chromosome Length In Grch37/Hg19 We have closed your question to allow us to keep similar content in the same thread. If you disagree with this ...
written 3.7 years ago by Chico Fernandez70
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Comment: C: Coordinates of centromers in human chromosomes
... Sorry, seems the stupid question. I will remove it. Thank you very much! ...
written 3.7 years ago by Chico Fernandez70
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(Closed) Coordinates of centromers in human chromosomes
... Hello, I would like to divide my chromosomes into two parts (shoulders of chromosomes) and do not take into account centromere region. How can I find coordinates of centromeres of all chromosomes? This answer: https://www.biostars.org/p/2349/ gives a solution only for several chromosomes... ...
centromers written 3.7 years ago by Chico Fernandez70 • updated 3.7 years ago by Chris Miller21k
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Comment: C: aCGH CNV detection
... But why r^2 is a misleading? You reported r^2 in your CNVKit paper, if I remember it correctly... (I read the paper you suggested and figured out why, sorry) ...
written 3.7 years ago by Chico Fernandez70
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Comment: C: RStudio crashed without warning in Windows 10
... Can you measure the amount of memory RStudio consumes during building a graph? It may be probably because of R is out of memory. Do you have similar problems with the same data, using other OS (on the same computer)? ...
written 3.7 years ago by Chico Fernandez70

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