Oxford Nanopore BWA MEM alignments

Question

[QVINTVS_FABIVS_MAXIMVS]

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"?

Answer 1

[WouterDeCoster]

According to the examples of Lumpy 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