I want to see an impact of the realignment step (GATK) on the variants in the variant calling. So, I have variants of the realigned reads (A) and variants of the not realigned reads (with out a realignment step) (B).
In order to see the difference between variants I build up differences A-B and B-A according to the positions of the variants.
My idea is that B-A difference will return me possible false positive variants. What appears in B and does not appear after a realignment in A should be caused by not detected indels in the reads and lead to the mismatches and after a realignment step it got fixed and the reads are shifted so that there are no mismatches anymore.
I guess I am pretty right about it B-A difference but I have problems with interpreting A-B difference. I thought that it could return me true positives that could be detected only after shifting the reads (after he realignment step).I have looked in IGV at the positions of A-B difference and have found that there were as well false positives, so that the reads got shifted and the were no mismatches in the alignment anymore. I guess my idea about A-B difference and true positives is wrong, isn't it?
Thanks in advance.