Hi all,

I have a quick question. 

When I run bwa mem for oxford nanopore with the option: 

    bwa mem -x ont2d 

Should I include the option: 

    bwa mem -x ont2d -M 

For split reads? If I want to run Lumpy on the alignments would I need to supply "-M"?
According to the [examples of Lumpy][1] you don't have to use `-M`:

    bwa mem -R "@RG\tID:id\tSM:sample\tLB:lib" human_g1k_v37.fasta sample.1.fq sample.2.fq \
        | samtools view -S -b - \
        > sample.bam


  [1]: https://github.com/arq5x/lumpy-sv
