I have an insertion in my genome and I want to identify the insertion site. As far as I understand I should find the read pairs where one read is mapped to my insertion sequence, but mate is unmapped. I found these reads using samtools:
samtools view -F 4 -f 8 alignment.sam > alignment_filtered.sam
Now I need to find the unmapped mates. How can I do that? As far as I understand I should then 'de novo' build the insertion site sequences (left and rigth from my insertion) using the unmapped mates. I would be grateful if anyone could suggest me the tool for that and also comment on the whole procedure I am using.
Thank you in advance