Question: Whole Genome Sequencing: Bwa
0
gravatar for mathiasf52
5.8 years ago by
mathiasf5220
mathiasf5220 wrote:

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 • 2.6k views
ADD COMMENTlink modified 5.8 years ago by Devon Ryan88k • written 5.8 years ago by mathiasf5220
1
gravatar for Devon Ryan
5.8 years ago by
Devon Ryan88k
Freiburg, Germany
Devon Ryan88k wrote:

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 COMMENTlink written 5.8 years ago by Devon Ryan88k
1

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

ADD REPLYlink written 5.8 years ago by Istvan Albert ♦♦ 79k

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 REPLYlink written 5.8 years ago by Devon Ryan88k

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 REPLYlink written 5.8 years ago by mathiasf5220

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 REPLYlink written 5.8 years ago by Sean Davis25k
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