Question: Can someone explain what the -M option in BWA-MEM does?
gravatar for James Reeve
14 months ago by
James Reeve90
James Reeve90 wrote:

I'm reading abput BWA for my project which involves SNP calling for whole genome pool-seq data. I've noticed a few online tutorials for BWA-MEM specify the -M option for a basic alignment. I don't understand what this option is doing.

Reading the manual it says;

-M Mark shorter split hits as secondary (for Picard compatibility).

What does 'split hits' mean?

What types of data should this option be used for?

bwa alignment • 760 views
ADD COMMENTlink modified 14 months ago by Devon Ryan91k • written 14 months ago by James Reeve90
gravatar for Devon Ryan
14 months ago by
Devon Ryan91k
Freiburg, Germany
Devon Ryan91k wrote:

"Split hits" here means chimeric alignments, otherwise known as "supplementary alignments", such as when part of a read aligns to chr1 and the rest to chr4. By default, bwa mem will set bit 0x800 for the shorter segments of such alignments. Apparently some versions of picard didn't like that and either break or throw an error. The -M option is supposed to set bit 0x100 (secondary alignment) instead. To my knowledge this isn't actually needed with remotely recent versions of picard.

ADD COMMENTlink written 14 months ago by Devon Ryan91k

So is -M just a way to adjust your output for Picard?

ADD REPLYlink written 14 months ago by James Reeve90


ADD REPLYlink written 13 months ago by Devon Ryan91k

Does this also include picard tools in GATK ?

ADD REPLYlink written 8 months ago by Mehulsharma.25310
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