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What to do with unpaired reads when calling variants?

monicafabbromonicafabbro ArgentinaMember

Hi guys!
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!!


Best Answer


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