Hi,
I am trying to use TarPan to view the newly analyzed Targeted Panel Sequencing data.
I use hg19 reference genome and the chromosome numbers start with "chr" prefix. While using the TarPan viewer, except the RCircos plot everything else look fine.
In R circos plot, initially it was not showing the translocations, then by adding
#if the chr prefix is on chrom, remove it
structvar$chrom <- gsub("chr", "", structvar$chrom)
at line 554 of server.R, it resolved that issue.
Even then, it is not showing the inter-chromosomal SV events.
I tried manually replacing all the chr prefix from the chromosome number for one sample, then it started to show the inter-chromosomal events to that samples. In this case "Inter-chromosomal SV" events can be viewed even without selecting the check-box.
Can you please explain me how to resolve this issue for vcf files with "chr" prefix in their chromosome number?
Hi, I am trying to use TarPan to view the newly analyzed Targeted Panel Sequencing data. I use hg19 reference genome and the chromosome numbers start with "chr" prefix. While using the TarPan viewer, except the RCircos plot everything else look fine. In R circos plot, initially it was not showing the translocations, then by adding
at line 554 of server.R, it resolved that issue. Even then, it is not showing the inter-chromosomal SV events. I tried manually replacing all the chr prefix from the chromosome number for one sample, then it started to show the inter-chromosomal events to that samples. In this case "Inter-chromosomal SV" events can be viewed even without selecting the check-box.
Can you please explain me how to resolve this issue for vcf files with "chr" prefix in their chromosome number?
Thanks Parvathi.