I have a .bam file with paired-ends alignments and, with GASVPro, I have predicted some structural variations. However, there is one thing I don't understand. First of all, this software clusters discordant paired-ends. In this step, GASV detects insertions. However, next step is when GASVPro adds the depth coverage information for an improvement in the reliability of the results. Here is when all my insertions disappears.
Why? My theory (maybe wrong theory) is the following one: for novel insertions, there will not be a difference in the coverage of the region I am evaluating and, because of that, there will not be support from the coverage and the insertion previously predicted will be set aside. Nevertheless, if the insertion is n adjacent repetition, there will be a change in the coverage of that region and, does this insertion will be placed into the final results?
I have read the manual but found no clue about it.