Question

Mismatch and Indel rate in alignment

0

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6.7 years ago

BDK_compbio ▴ 140

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.

alignment sam bam • 2.6k views

ADD COMMENT • link updated 6.7 years ago by prasundutta87 ▴ 660 • written 6.7 years ago by BDK_compbio ▴ 140

score 1 · Answer 1 · 2017-08-29

1

Entering edit mode

6.7 years ago

prasundutta87 ▴ 660

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

ADD COMMENT • link 6.7 years ago by prasundutta87 ▴ 660