I have some paired end exome sequencing, and after checking out the samples in fastqc, I found there was an enrichment for Illumina adapters. I used Trimmomatic to remove the adapters (using Illumina Clip), which gives me paired reads, and unpaired reads for forward and reverse respectively post trimming.
I'm following the GATK best practises for variant calling, which recommends BWA MEM for alignment. I can use the paired, trimmed reads for to align, but there's quite a large proportion of reads which are trimmed and unpaired. The bedrock of my question is how can I use these effectively?
Would the best way be to do an alignment with the pairs, then unpaired, and combine the SAM files in some way? Or even merge the BAMs?
Anyone had a similar experience? Advice is welcome!