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
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?