Manually correct heterozygous indels

[captainobvious]

Hi there!

Does anyone know how to deal with heterozygous indels manually? I don't know how to deal with cases where sequence in one direction shows double peaks while the sequence in the opposite direction shows NO peaks at those sites. I'm thinking that it would be right to ignore those peaks. I could be wrong. I'm just not sure...

[swbarnes2]

Make two reference sequences, one with the indel, one without. The reads that best align to the indel will align to that sequence, the ones without will best align to the other.

That'll help you figure out of the reads are real.

[captainobvious]

Ok, I thought that would be the way to go. Just wanted a second opinion. Thanks!!!