BWA-mem2 mem M option
Hi, everyone!
I am new to the gatk pipelines, so I'm not sure is it necessary to use the -M option in the bwa-men2 commond before I put the outcoming bam file to the gatk mutect pipelines for calling the mutation variants?
I have read some post about the supplementary alignment and secondary alignment, I'm still confused, is there big difference between the gatk mutect pipelines whether I use the -M option or not, which one is recommended for gatk?
I have do both, with the -M option and without, in one sample with all other command the same to call for the mutation variants, there are some different between the two outcomes, such as the number of variants detected.
Here is my command of bwa-men2:
bwa-mem2 mem -M -t 16 -R "@RG\tID:${id}\tSM:${id}\tLB:WXS\tPL:Illumina" ${INDEX} ${fq1} ${fq2}
Thank you!!!
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Hi bella kira
-M option in bwa mem is no longer necessary since those earlier incompatibilities with picard are long gone, though the choice is yours to make whether to use it or not. (Beware that -M may produce out-of-spec bam files. )
If you would like to get some more insight into whether others are using this option or not you may take a look at the below articles
https://www.nature.com/articles/s41467-018-06159-4
https://github.com/CCDG/Pipeline-Standardization/blob/master/PipelineStandard.md
Regards.
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