I have a weird question.
I have been running a WES pipeline which has been made by someone else. And, they decided to use trimmomatic for the adapter trimming step which produces both:
*.paired.fastq.gz and *.unpaired.fastq.gz
And, these files are processed by BWA-MEM one by one and then the bam files are merged into one by using Picard merge. Apparently, this step was added because it increases the coverage of variants and the sequencing coverage.
My question: In your opinion, is it wise to merge paired and unpaired bam files? Do you think it will have an adverse effect on the variant quality? Can I skip this step and only use paired files?