I've been using the IGV to check quality of alignments of illumine sequences genomes, and to extract the consensus sequence for a particular gene of interest for population analysis. however when bringing the sequences together in mega I noticed that IGV had not included insertions in the consensus sequence, and so a few of the amino acid haplotypes were wrong and i'm having to painstakingly correct the sequence manually (fortunately the gene is quite short).
Looking at the IGV manual I could not find a way of retrieving the matrix from which consensus is calculated (even though it states the matrix is also copied to the clip board). Can anyone let me know how to get the matrix? and is there a method of retrieving consensus sequence of a specific region of a bowtie2 aligned .bam file that does include indels?
Thanks for any help. :)