[Bioc-devel] IGV VCF demo, other suggestions? [was Re: IGV - a new package in preparation]

Paul Shannon paul.thurmond.shannon at gmail.com
Tue Mar 13 01:20:02 CET 2018

Gabe and Levi made a good case for supporting GRanges in IGV.   Looking at the GenomicRanges vignettes, it appears that many of Herve’s introductory examples have GC content as the mcols column of interest.   Would that be a good test and demo for IGV?  Or perhaps some other genomic quantity,  one for which sample data is already present in some Bioconductor package’s extdata?

The IGV VCF track now works, using GenomicRanges and VariantAnnotation.  It might be of interest, maybe lead to more useful suggestions which would be good for me to hear at this stage.   Here is a code chunk using default parameters for colors, track height and etc.  Homozygous non-reference calls are rendered in light blue, heterozygous in dark blue, reference in gray.

igv <- IGV(portRange=9000:9020)
setGenome(igv, “hg19")
setBrowserWindowTitle(igv, “VCF demo”)

f <- system.file("extdata", "chr22.vcf.gz", package=“VariantAnnotation”)
chrom <- “22"
start <- 50586118
end   <- 50633733

rng <- GRanges(seqnames=chrom, ranges=IRanges(start=start, end=end))
vcf.sub <- readVcf(f, "hg19", param=rng)

track <- VariantTrack(“chr22-tiny", vcf.sub)
displayTrack(igv, track)
showGenomicRegion(igv, sprintf("chr22:%d-%d", start-1000, end+1000))


> On Mar 9, 2018, at 4:15 AM, Levi Waldron <lwaldron.research at gmail.com> wrote:
> Definitely +1 for supporting GenomicRanges, including what's in genome() and mcols(). There's a demo of an rtracklayer -> GRanges -> UCSC 

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