User: bernatgel
bernatgel • 2.0k
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Posts by bernatgel
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... Hi @aiswaryabioinfo
You can use [karyoploteR](http://bioconductor.org/packages/karyoploteR) as @RamRS has suggested with this data and it can do what I think you are requesting.
The first you need is to read the data and make a GRanges with the genes
library(karyoploteR)
#read the ge ...
written 4 days ago by
bernatgel • 2.0k
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... Hi @ma23,
You have a few problems with your code, starting by the fact that you are reading the data twice and grepping for "#CHROM" and the header line starts with "CHROM" without hash, so it won't detect it.
Basically, if you have a headerless vcf and only want to create a GRanges to plot the ...
written 14 days ago by
bernatgel • 2.0k
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Comment:
C: KaryotypeR for germline mutations
... Hi @ma23
Can you show us a few lines of the VCF? and the exact code you are using? ...
written 18 days ago by
bernatgel • 2.0k
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... You can also give a try to [karyoploteR](http://bioconductor.org/packages/karyoploteR/). It's also an R/Bioconductor package with a different approach to plotting data along the genome. And it can work with any genome, including "dm6".
There's a [karyoploteR tutorial](https://bernatgel.github.io/ka ...
written 21 days ago by
bernatgel • 2.0k
2
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... Your command has a typo! it should be "chromosome" and it's "chrmosome" (missing first o) so it thinks you have specified no chromosome at all. ...
written 21 days ago by
bernatgel • 2.0k
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... To produce something similar to the second figure you can use [karyoploteR](https://bernatgel.github.io/karyoploter_tutorial/). ...
written 7 weeks ago by
bernatgel • 2.0k
0
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... Hi Sara,
If you have shallow WGS you'll probably want to plot a whole genome view or at least a chromosome-wide view. You can create these plots in R with [karyoploteR](http://bioconductor.org/packages/karyoploteR/) using the `kpBAMDensity` function:
library(karyoploteR)
bam.file <- "pa ...
written 8 weeks ago by
bernatgel • 2.0k
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Answer:
A: Annotating varscan2 output
... We have used [annovar](http://annovar.openbioinformatics.org/) to annotate VarScan results in VCF. It works quite well and is widely used.
You'll need to decide what you want to annotate and download the annovar databases from the [annovar website](http://annovar.openbioinformatics.org/en/latest/u ...
written 9 weeks ago by
bernatgel • 2.0k
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... Hi @hektor102
I agree with Kevin on asking your colleagues why the AB notation is needed since it's less informative than the actual alleles, specially using Illumina definition of A and B.
If you are referring to the A and B alleles **as defined by Illumina** for their SNP-array technology, then ...
written 9 weeks ago by
bernatgel • 2.0k
2
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398
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... You can use [karyoploteR](http://bioconductor.org/packages/release/bioc/html/karyoploteR.html) as Bastien suggested, but if you can a whole genome coverage plot I think the best approach would be to perform a bit of preprocessing instead of going directly to `kpPlotCoverage`.
I would recommend usi ...
written 4 months ago by
bernatgel • 2.0k
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