Closed AndreaG5 closed 2 years ago
Hi Andrea,
Thanks for reporting the issue. Would it be possible for you to provide VCF examples (both the RO/AO and AD you have tried) so I can test them in deep? VCF with one or two variants should be enough :)
José Marcos.
Hi!
I hope I selected the correct vcf :D (I tried with multiple ones, so I hope these two are the right ones). I attach them: 1) _original.vcf --> as the name states it's the original vcf file output of IonTorrent. 2) _edited.vcf --> is the one that I edited to create "AD" field.
Both were read without apparent errors so I believe they're correctly formatted.
Text me if any problem occur! Thank you so much
Andrea
Hi Andrea,
Thanks for the files. After checking them, I have observed that The Torrent Variant Caller produces the VCF in a slightly different way. I am planning to push a new version in a few days to fix this issue. I am also considering to automatically support Torrent Variant Caller VCFs, assuming AO and RO are common fields when using TVC. I'll let you known when the new version is available :)
José Marcos.
I guess so, I mean, I carefully read tool documentation and I think AO and RO are the most appropriate ones.
Thank you so much and I'll wait for next drop! :)
Andrea
Hi Andrea,
CNVfilteR has been updated. Please, use last version (1.6.2) to make it work:
vcfs <- loadVCFs(vcf.files, cnvs.gr = cnvs.gr, ref.support.field = "RO", alt.support.field = "AO")
Additionally, development version (so next Bioconductor release) will automatically recognize Torrent Variant Caller VCFs.
I would very appreciate if you can confirm that the fix is working properly.
Hi @jpuntomarcos,
I just tried this new version and I can confirm that everything seems to work properly! :)
If I'll find something unclear I'll text you again.
I really appreciate your quickness in response and fix!! Have a good day!
You are welcome :)
J.
Hi, I am trying to run CNVfilteR on IonTorrent data. The .vcf is the output of Ion software so I cannot do so much on it. Reading the manual I've found that is possible to adapt the function to whatever just adding some informations. I correctly generate loadCNVcalls object.
So, following the manual I tried to launch the following after checking the FORMAT fields in my.vcf. 'RO' stands for Reference observed and 'AO' for allele observed (integers of reads)
It results me in an error:
Error in depths.alt + depths.ref : non-numeric argument to binary operator
So, following the manual and checking the example data from the package I decide to scripting to create a new FORMAT field, called 'AD' which was the concatenation of 'RO' and 'AO', e.g. RO=5, AO=50 --> AD=5,50. I added to headers too and then launch:
It doesn't give me any error, but the result object is empty in 'metadata' field, so it seems like he's not able to parse anything(I attach a partial screenshot of the output).
I wonder why this happens and if you have any suggestion to give. I'm available for any further info. Thanks very much,
Andrea