Mismatch setting in BWA

genelab · 08-01-2010, 01:36 AM

Helllo everyone,

I am still comfused how to set the maximum mismatch to 2 when I use "bwa aln", given 75bp reads.

bwa aln -n 2
or
bwa -l 75 -k 2

Any suggestions will be highly appreciated

genelab · 08-03-2010, 06:12 PM

could anybody help me to answer this question? thanks!

adamdeluca · 08-03-2010, 07:14 PM

Those are equivalent for 75 bp reads.

genelab · 08-03-2010, 10:59 PM

Quote:

Originally Posted by adamdeluca

Those are equivalent for 75 bp reads.

How about the read length not equal to 75, such as 50 or 100bp?

Thanks for your kindly reply

adamdeluca · 08-04-2010, 05:02 AM

-n 2 is equivalent to -l READ_LENGTH -k 2

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08-01-2010, 01:36 AM	#1
genelab Member Location: honston Join Date: Nov 2009 Posts: 27	Mismatch setting in BWA Helllo everyone, I am still comfused how to set the maximum mismatch to 2 when I use "bwa aln", given 75bp reads. bwa aln -n 2 or bwa -l 75 -k 2 Any suggestions will be highly appreciated Last edited by genelab; 08-03-2010 at 06:10 PM.

08-03-2010, 06:12 PM	#2
genelab Member Location: honston Join Date: Nov 2009 Posts: 27	could anybody help me to answer this question? thanks!

08-03-2010, 07:14 PM	#3
adamdeluca Member Location: Iowa City, IA Join Date: Jul 2010 Posts: 95	Those are equivalent for 75 bp reads.

08-04-2010, 05:02 AM	#5
adamdeluca Member Location: Iowa City, IA Join Date: Jul 2010 Posts: 95	-n 2 is equivalent to -l READ_LENGTH -k 2