Question

Bwa Commands

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11.1 years ago

shilpy ▴ 20

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 • 2.5k views

ADD COMMENT • link updated 11.1 years ago by SES 8.6k • written 11.1 years ago by shilpy ▴ 20

score 3 · Answer 1 · 2013-03-29

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11.1 years ago

Surya Saha ▴ 260

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.

ADD COMMENT • link 11.1 years ago by Surya Saha ▴ 260

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

ADD REPLY • link 11.1 years ago by shilpy ▴ 20