Added option to filter for af difference during harmonization with gnomad
by default, indels are not flipped in meta-analysis
There's now a new flag --flip_indels to enable flipping of indels during meta-analysis to try aligning variants. It was observed during analysis of 3-way meta results that the indel flipping and matching can cause mismatching variants aligned.
Also a minor structural change to meta_analysis.py was to combine functions is_equal and equalize_to since they were pretty similar.
There's now a new flag
--flip_indelsto enable flipping of indels during meta-analysis to try aligning variants. It was observed during analysis of 3-way meta results that the indel flipping and matching can cause mismatching variants aligned.Also a minor structural change to meta_analysis.py was to combine functions
is_equalandequalize_tosince they were pretty similar.