settings optional parameters bwa mem

Question

[juli396]

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

[Sej Modha]

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.

[juli396]

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...

[mforde84]

https://software.broadinstitute.org/gatk/best-practices/

Answer 1

[Devon Ryan]

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.

[i.sudbery]

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.

[Devon Ryan]

Possibly also -R for a read group.