search

vplagnol / ExomeDepth

ExomeDepth R package for the detection of copy number variants in exomes and gene panels using high throughput DNA sequencing data.
59 stars 26 forks source link

Error in Exomedepth CallCNVs function #26

Closed Shrutik08 closed 4 years ago

Shrutik08 commented 4 years ago

Hi,

I was running Exomedepth package for cnv detection from germline CNV's, its running fine till RData file creation but it is throwing an error when its running CallCNVs function, the error is:

Now computing the likelihood for the different copy number states Error in CallCNVs(x = all.exons, transition.probability = 10^-4, chromosome = refcounts.dafr$space, : Chromosome, start and end vector must have the same lengths.

Can you please explain what this error means? I am not able to debug this error, this will be very helpful.

vplagnol commented 4 years ago

mmmm... Not sure. Can you please run a head(refcounts.dafr) and tell me what you see? I wonder if space should now be seqnames or something like this.

Shrutik08 commented 4 years ago

Hi Vincent,

Yes I checked, space should be seqnames actually I aws using the latest exomeDepth version and the attributes/header details that I am using are of old version, so its throwing an error.Thanks alot for your help. Thanks for your quick response.

The issue is fixed now.

Thanks & Regards Shruti Kapil

On Sun, Apr 5, 2020 at 8:14 PM Vincent Plagnol notifications@github.com wrote:

mmmm... Not sure. Can you please run a head(refcounts.dafr) and tell me what you see? I wonder if space should now be seqnames or something like this.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/vplagnol/ExomeDepth/issues/26#issuecomment-609427179, or unsubscribe https://github.com/notifications/unsubscribe-auth/AOT3MTCEYM3VDKPQCFQNLTDRLCKM7ANCNFSM4L2BPT3Q .