Hi all,
We have designed IDT probe to enrich the target region for tumor samples, including intron regions of known fusion genes.
We have tried several fusion detection tools, such as delly, manta, genefuse to determine the fusion status, however, we found delly and manta were sometimes lack of sensitivity, especially for ctDNA based data. While genefuse was too sensitive, which always gave noise/false fusion results. And genefuse can not determine structure variants such as exon deletion (MET EXON14 SKIP).
Can anyone help?
Thanks, Junfeng
will have a try, and response if have any question
Hi Kevin,
Any suggestions for the input bam? Since unproper mapped reads might be removed during alignment, what kind of bam file should I used?
I tried raw data mapped file or markdup one, without any result, while delly or manta can give out.
Inless you've got a weird aligner, or using non-default settings, unmapped reads will still be in the BAM file - they'll just be marked as unmapped.