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Question: Are there maximum Penalty Scores in BWA-MEM?
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gravatar for Mesohexaploid
12 months ago by
Mesohexaploid • 10
Mesohexaploid • 10 wrote:

Apologies if this is a simplistic question, I am new to Galaxy.

I am working on a variant calling workflow for paired DNAseq reads, with BWA-MEM as my aligner. Since I have custom parameters, I would like to manually enter them into BWA-MEM through the "Select full list of options" category.

I was just wondering if there are any maximum values for scoring I should adhere to. For example, if I want an ungapped alignment, what's the highest penalty score I can assign to -O? In the bwa manual, there are values in square brackets behind each argument, but I'm not sure what they represent. The default settings?

alignment bwa-mem bwa • 347 views
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modified 11 months ago • written 12 months ago by Mesohexaploid • 10
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gravatar for Mesohexaploid
11 months ago by
Mesohexaploid • 10
Mesohexaploid • 10 wrote:

Hello again, I'm just going to answer my own question here in case there is anyone else who would like to know the answer to this (doubtful).

I asked this question in the non-Galaxy Biostars, and basically, there are no maximum penalty scores and the scores in the square brackets represent the default values.

The best way to generate an ungapped alignment is to set the penalty value for a gap (-O) really high, like to 100, while keeping all other settings default. This should result in BWA-MEM dropping a seed extension as soon as a gap is encountered.

ADD COMMENT • link written 11 months ago by Mesohexaploid • 10
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