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settings optional parameters bwa mem

Hello,

I have NGS targeted sequencing data, human data. I need to alignment data with BWA-MEM. Can you help me how to set optional parameters for my data? Do you have some experience or idea?

Thank you for you answer

sequencing alignment
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updated by Biostar Biostar • written by juli396 • juli396

It would be helpful if you provide more details about what you are trying to achieve. For general parameter and options available in bwa refer to bwa manual.

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written by Sej Modha Sej Modha

After I want to detect mutations. (I have data with acute leukemia). I think you have maybe some experiences with human data and you have some advices for optimal parameters for processing human data. I thought it is different setting parameters for human data or some plants or some animals...

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written by juli396 • juli396

1 answer

As a rule of thumb when using a new tool, run it with all of the default parameters, changing only the number of threads. Only start changing parameters if the results don't look reasonable.

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written by Devon Ryan Devon Ryan

If you plan to use the GATK pipeline downstream, I think you will need to use the -M option to BWA-MEM to make the BAMs it outputs compatible with Picard.

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written by i.sudbery i.sudbery

Possibly also -R for a read group.

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written by Devon Ryan Devon Ryan

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