arshajii/ema-paper-data

Data and resources for EMA paper

ema-paper-data's Issues

Question on homologous regions

Hi,

I ran BWA, LongRanger, and EMA for NA12878 WGS dataset from https://support.10xgenomics.com/genome-exome/datasets/2.1.4/NA12878_WGS_v2, and looking at the challenging regions listed in your notebook:

C4A 6:31965242

AMY1 1:104197843

CYP2D7 22:42537120

It looks like EMA has a higher coverage in those regions, however all those extra alignments are secondary (shaded on the screenshot). I'm wondering if that's an expected picture for EMA? And those secondary alignments could not be resolved via the linked read information? As far as I understand, those secondary alignments will be ignored by variant callers. They look to add up noise in variation, as in this CYP2D6 screenshot (more vertical colored lines at the coverage tracks):

Please, correct me if I'm wrong. I see you evaluated those regions with a more sophisticated strategy by checking against the NA12878 assemblies, so probably I'm not looking at these regions the right way.