I have used Trimmomatic to filter my raw reseq data into clean one. However, the read length I got from Trimmomatic ranges from 36 to 150. I wonder whether it is reliable to detect SV, CNV etc through BreakDancer, CNVnator,etc using the reseq data set with different read lengths. Because the proper estimation of the insert size may affect the performance of BreakDancer to detect SVs. I am not sure whether the read length would affect or not.
Thanks in advance!