Dear all, i've encountered a problem using CLC genomics workbench analysing Illumina targeted data.

I'm using Illumina MiSeq with Haloplex and obtain 2 .fastq files for each sample. When i'm importing data, usually i don't activate "paired data" switch and proceed to align the two file vs hg19 obtaining a very good variant detection and more than 99% of coverage @ 20x. If i activate "paired data" when importing .fastq files coverage goes down to 93% in some genes composing my panel. Is it a normal behaviour? can be related to the haloplex library?

thanks!