Alignment filters ?

https://github.com/google/deepvariant/issues/914

min_mapping_quality - If the MAPQ value of the read is below a pre-set value, the read is not included for subsequent analysis. By default, that value is 5 for WGS and WES with BWA, it is 0 for vg-mapped files. It is 1 for PacBio and ONT reads.

min_base_quality - If the base quality value at the variant position considered is below a pre-set value, the read is not included in the analysis of that specific variant position (it could be included for other positions if the base quality of the base at the other position is higher). For SNPs, the direct position is considered. For Insertions, the behavior depends on other flags, in some cases averaging qualities of inserted bases, in other cases looking at the minimum base quality value. By default this is 10.

downsampling - When coverage is very high, random downsampling is applied to reads for inclusion into the pileup that the neural network sees.
deepvariant 默认情况下使用使用MAP==5过滤WGS数据， MAP==1过滤ONT和Pacbio数据。