Question: Mismatch and Indel rate in alignment
0
gravatar for sbdk82
2.3 years ago by
sbdk8260
United States
sbdk8260 wrote:

I am using BWA to align the raw reads against a contig set. I would like to know the overall mismatch rate as well as indels in the entire alignment (SAM/BAM). I tried various options of samtools/bamtools, but could not able to find this.

bam sam alignment • 1.3k views
ADD COMMENTlink modified 2.3 years ago by prasundutta87360 • written 2.3 years ago by sbdk8260
1
gravatar for prasundutta87
2.3 years ago by
prasundutta87360
prasundutta87360 wrote:

check this out Mismatch and Indel statistics from BAM/SAM file

ADD COMMENTlink written 2.3 years ago by prasundutta87360
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