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Bwa Commands

While aligning normal data using bwa how to set seed length to 50 and the number of mismatches allowed within the seed to 2. I am doing as following...not sure bwa aln -l chr22.fa normal_read.fastq > normal.sai

samtools
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updated by SES SES • written by shilpy • shilpy

1 answer

Try

bwa aln -l 50 -k 2 chr22.fa normal_read.fastq > normal.sai

See http://bio-bwa.sourceforge.net/bwa.shtml for more details.

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written by Surya Saha Surya Saha

Thank you very much Surya, I was looking same link unfortunately not able to figure it out.

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written by shilpy • shilpy

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