Question: Question About Bwa Aln Handled The Indel Size
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gravatar for ge.yunqing90
5.3 years ago by
ge.yunqing900 wrote:

I have dataset which is exome-seq, and I am planing to use bwa aln for alignment with its default values, and use the GATK for indel / snp information. I checked the bwa manual which didn't show anything about indel size. If I set the -n value 2 mismatch, then lot of my reads with larger indel size > 2 will not be able to map on the reference genome. I heard the parameter bwa mem doesn't have this limitation and it can handled a larger indel size.

Thanks in advance!

Ge

bwa • 1.5k views
ADD COMMENTlink modified 5.3 years ago by swbarnes25.5k • written 5.3 years ago by ge.yunqing900
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gravatar for swbarnes2
5.3 years ago by
swbarnes25.5k
United States
swbarnes25.5k wrote:

I've seen bwa correctly map a read with a 10 base pair deletion, but it was only able to do this because the mapping position of the mate kicked on the Smith-Waterman mapping for that read.

ADD COMMENTlink written 5.3 years ago by swbarnes25.5k
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