Trimmomatic options for Novaseq WES and samqualfilter? or filter by qualty in sam files

Hello , I am having headaches regarding this sample.

I am performing WES for calling SNP and CNV. All was good until I wanted to show the coverage by gene or fragment. Comparing my results with other ones, I found no coverage by the region I wanted, compared with the results I stand “for gold standard” (indeed they are from a bioinformatics company).

I ask them what happens, and they told me that may be the mistake come from the previous step to the alignment with BWA-MEM

Thus, the reads are 100 bp, and the adapters are CTGTCTCTTATACACATCT+AGATGTGTATAAGAGACAG. Looking at the fastq files is a Novaseq instrument. But only on the fastq is this sequence: AGATGTGTATAAGAGACAG (as adapter)

Furthermore, on my fastqc results, it says that there is no adapters sequence. (and the other sections are OK)

However, the per-base sequence content looks like this.:

Another question is if there are samqualfilter tool, or it is propiertary from the company? Because I googled and I can’t find anything.

Please, if anyone knows how to proceed with trimming step on WES (Novaseq) by “smoothing” this graph and the optimal parameters I would be very grateful.

Thanks