cfDNA ultra-deep sequencing with UMIs
I am analyzing sequencing data from a capture panel which uses UMIs. I did ultra-deep sequencing to detect variants in a very low VAF (less than 1%). This is an already fragmented DNA coming from plasma.
After doing my pipeline using fgbio, I realized that I have multitude of reads with the same start/end and different UMIs, so they are called as different families. This is not too rare to me for the wild-type reads. But for ultra-rare mutations, it is difficult to me to understand that there are 5 reads (fragments) with the same start/end and different UMIs (different in all positions, not just one base). That woud mean that these 5 DNA fragments have been cut exactly in the same positions. Does anyone have an explation for this? Is there anything incorrect in our pipeline?
• 120 views
Read more here: Source link