Using the -Az flags gives incorrect coverage information.

[peterpru]

Hi, I have created d4 files both with and without the -Az flags, and it seems that the compression flag leads to dips in coverage in the mitochondria. Below an example of the same file run with and without the flags for the same region:

No flags:

MT	7440	7441	677191
MT	7446	7447	688499
MT	7447	7448	685584
MT	7448	7449	690872
MT	7449	7450	693282
MT	7450	7451	693882
MT	7451	7452	693211
MT	7452	7453	693159
MT	7453	7454	693898
MT	7454	7455	687249
MT	7455	7456	684610
MT	7456	7457	683905
MT	7457	7458	686301
MT	7458	7459	683167
MT	7459	7460	687118

With flags:

MT	7446	7492	1
MT	7492	7497	2
MT	7497	7498	3
MT	7498	7502	4
MT	7502	7503	10
MT	7503	7504	4114
MT	7504	7505	7941
MT	7505	7506	12341
MT	7506	7507	16501
MT	7507	7508	29745
MT	7508	7509	32616
MT	7509	7510	37264

Here I have a bad excel graph showing two of these dips, they seem to be around SNVs. Maybe it is certain flags in there reads that are causing them to be excluded, however in IGV the reads look as normal.