Question: Oxford Nanopore BWA MEM alignments
4
gravatar for QVINTVS_FABIVS_MAXIMVS
3.1 years ago by
USA SoCal
QVINTVS_FABIVS_MAXIMVS2.4k wrote:

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"?

ADD COMMENTlink modified 3.1 years ago by WouterDeCoster43k • written 3.1 years ago by QVINTVS_FABIVS_MAXIMVS2.4k
7
gravatar for WouterDeCoster
3.1 years ago by
Belgium
WouterDeCoster43k wrote:

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
ADD COMMENTlink written 3.1 years ago by WouterDeCoster43k
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