Generating a consensus sequence

[Sophie Frances]

Hi, I need to export a consensus sequence from IGV for downstream analysis and I have noticed that my samples have an artefact where there is an insertion at a specific position. An example is where some reads have up to 3 bases inserted but the vast majority do not I get either an N (where no base is dominant) or the base that comprises >50 %. For instance at one locus  37532 reads have no insertion but 1256 have a G (others are 209 with A, 342 with C and 207 with T). THe result is that instead of no insertion, I hvae an insertion of "T" in the consensus. Clearly the majority of sequences have no insertion, so no insertion would be a more accurate reflection of the data. Is there any way to change this ? I can't see anywhere how to change settings for generating a consensus. 

THanks a lot ! 

1b:257
G

Total count: 2014
A : 209 (10%, 182+, 27- )
C : 342 (17%, 235+, 107- )
G : 1256 (62%, 736+, 520- )
T : 207 (10%, 137+, 70- )
N : 0
---------------
DEL: 37532
INS: 0

[igv-help]

Hi,

You can't do that with IGV,  as you've discovered.  IGV is primarily a visualization tool,  I suspect there might be better tools for generating consensus sequence.