Identify how many inserts mapped to a region
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18 months ago

Hi, good day. I am struggling looking for the insert mapped in my alignment.

I did this samtools view SRR5882792_thaliana.bam 2:15186040-15186852 | head

I saw in the CIGAR table that there are only perfect matches like 100M but none with I which indicates insertion

I just wanna ask if the insert mapped is the same as insertion?

or is there any other way to find the insert mapped in a bam file?

Thanks :)

samtools insert map insert mapped bam • 289 views
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What's your understanding of "insert mapped"?