Whole Genome Sequencing: Bwa

Question

[mathiasf52]

Hi all,

I want to use BWA for aligning human WGS paired-end data generated by Illumina. I read the manual of BWA but I wonder which options are more important to consider for WGS alignment?

Thanks m

Answer 1

[Devon Ryan]

You don't actually have to change any options, the defaults should generally work fine (with the exception of number of threads to use, which will depend only on your hardware). Have a look at the results and then see if changing some of the options might make things better.

[Istvan Albert]

beyond the defaults there are different alignment modes that are important: aln, bwasw, mem

[Devon Ryan]

True, I was taking a strict interpretation of the question, but it would be wise for the original poster to think wisely about those.

[mathiasf52]

Thank you for your reply! actually I didn't well understand the options for "gap"... I want to analysis structural variants at the end ? should I consider any of gap options in the beginning?

Thank you

[Sean Davis]

Probably not. However, you will need to think about whether or not you need chimeric alignments. If so, then you are limited to using bwasw or mem as the alignment modes.