Hello,

I want to store detect my variants in a VCF format. For that I need to map my PE reads (100x2) to reference. What I have discovered however is that for a lot of my PE reads, the fragments size is smaller than 200bp, which means some PE reads overlap, increasing the coverage of a region artificially.

I thought I would merge the PE reads with SeqPrep to place all PE reads that overlap in a merged.fastq file.

My question is, how do I then map both unmerged PE reads and merged SE reads to the genome with bwa? I only know how to do it if it's only SE or only PE.

Also, does this approach sound reasonable? Adrian