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What to do with unpaired reads when calling variants?
I have filtered the adapters from my Illumina PE reads with Trimmomatic. This was the output (as I expected): sample.R1.trimmed.fastq, sample.R2.trimmed.fastq, sample.R1.unpaired.fastq and sample.R2.unpaired.fastq.
Then I aligned, separately, the trimmed.fastq pair and the unpaired.fastq with BWA mem.
The thing is that I am not sure if I have to merge my trimmed.bam with the unpaired.bam to get a final .bam and then start the GATK pipeline to call variants.
What do you suggest me to do in order to work with the correct .bam?
Thanks in advance!!