Extracting Indels from two aligned DNA sequences

Question

[manishagupta293]

How i can extract Indels out from two aligned DNA sequences using python or biopython?

Answer 1

[Hussain Ather]

SeqFIRE does what you want https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3394284/

Otherwise you could use samtools view to view them.

samtools view -h in.bam  \
| awk '$1 ~ "^@" || $6 ~ "I|D"' \
| samtools view -b - > out.bam

[manishagupta293]

SeqFIRE use protein alignments. But we want to use DNA alignment only. Is their a way to extract indels using BioPython?