My question is not a straight forward how to plot a circos plot of structural rearrangement data. I have checked more than 2 threads about this topic
But nearly all of the algorithms were based on the bam input. My problem is different than the common questions. I have obtained ~250 patient's ( Prostate Cancer) mutation files from ICGC. (vcfs for SNV,INDEL and structural variants). My aim is to get, TMPRSS2:ERG fusion positive/negative information from these vcfs. Since all the methods require a bam file, I simply thing there must be a way to get this information without downloading vcfs.
So I would be glad if you could answer the following;
Is there a way to scan this without visualising and checking by eye. —> I wanted to see by eye because for some patients, there are deletions in TMPRSS2 and ERG and I thought may be it is a low quality translocation therefore annotated as deletion.
I also have a bedpe format data, if there is a way related with this data format, I can also give it a shot.
Any help would really be appreciated. I have been working for this a quite long time so please forgive my frustration.