Closed beginner984 closed 5 years ago
If you already have a script to do this, why not just run that script?
I have been given a ruby script to convert .vcf to BEDEP
StructuralVariantAnnotation
can do this entirely in R.
vcf = readVcf("candidateSV.vcf.gz`)
bpgr = breakpointRanges(vcf)
R script to get this annotation
info(vcf)
findOverlaps()
on the breakpoint GRanges object. Something like:bpgr$MobileElement = ""
hits = findOverlaps(bpgr, me_gr, ignore.strand=TRUE)
bpgr$MobileElement [queryHits(hits)] = me_gr[subjectHits(hits)]$mobile_element_annotation
StraucturalVariantAnntoation
in a future release.I am very bad in coding
Everyone was bad when the first started. Keep learning :)
Sorry to be this much silly
I have been asked to visualize SV data; You please imagine I have a tumor and its matched model (organoid). I have called SV by Manta (my .vcf files are here)
https://www.dropbox.com/s/mhr63rn6v0fx89k/t_005.vcf?dl=0
https://www.dropbox.com/s/80o836njwgnw81k/o_005.vcf?dl=0
How I can get this picture from this paper
https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006596
Even code for producing this picture is here
https://github.com/DGendoo/PDACDiseaseModels/tree/master/SV/PrimaryPairs
But I don't know how use these scripts to produce such picture of my .vcf files
Could you please help me?
As issue does not involve a bug, feature request, or documentation issue with the StructuralVariantAnntoation package, this issues list is not the appropriate location for this question. Whilst I disagree with the approach to SV analysis taken in that paper, I consider that the complexity of analysis and the depth of understand required to produce the figure you have shown sufficient to warrant an authorship position on the paper in question. That said, just blinding reproducing the same figure on different data is more straight-forward but by no means trivial. I recommend you break the figure down into each component and tackle these one at a time, starting with panels A and B.
This question is much better suited to biostars.org or seqanswers.com
Hi,
I have called SV by Manta, how I could get this specific formats for my .vcf files please?
I have attached a sample .vcf and a desired annotation
LP2000104-DNA_A01_vs_LP2000101-DNA_A01.SVannotated.txt
candidateSV.vcf.gz
I have been given a ruby script to convert .vcf to BEDEP then R script to get this annotation but I am very bad in coding
So, I am wondering if I could get this annotation at all