Can reseq data set with different read lengths generated from Trimmomatic be used to detect SV, CNV etc through BreakDancer, CNVnator, Pindel etc?

Question

[zhengyunchaosky]

Hi,dear all,

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!

[trausch]

Read-depth methods should work fine because they usually just bin the read counts. For paired-end SV detection methods you probably should make sure that both pairs pass all your Trimmomatic filters.Insert size estimation is usually done using the outer insert size for a normal short-insert illumina paired-end so this should be robust against read-length variations.