Question

Whole Genome Sequencing: Bwa

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11.5 years ago

mathiasf52 ▴ 20

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

bwa • 4.4k views

ADD COMMENT • link updated 11.5 years ago by Devon Ryan 104k • written 11.5 years ago by mathiasf52 ▴ 20

score 1 · Answer 1 · 2013-05-28

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11.5 years ago

Devon Ryan 104k

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.

ADD COMMENT • link 11.5 years ago by Devon Ryan 104k

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

ADD REPLY • link 11.5 years ago by Istvan Albert 102k

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

ADD REPLY • link 11.5 years ago by Devon Ryan 104k

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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

ADD REPLY • link 11.5 years ago by mathiasf52 ▴ 20

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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.

ADD REPLY • link 11.5 years ago by Sean Davis 27k