Variant Hard Filtering
The default filters in the germline pipeline are as follows:
##FILTER=<ID=DRAGENHardQUAL,Description="Set if true:QUAL < 10.4139">
##FILTER=<ID=PloidyConflict,Description="Genotype call from variant caller not consistent with chromosome ploidy">
##FILTER=<ID=lod_fstar,Description="Variant does not meet likelihood threshold (default threshold is 6.3)">
| • | DRAGENHardQUAL–For all contigs other than the mitochondrial contig, the default hard filtering consists of thresholding the QUAL value only. |
| • | lod_fstar–For the mitochondrial contig, the default hard filtering consists of thresholding the LOD score only. |
| • | PloidyConflict–This filter is applied to all variant calls on chrY of a female subject, if female is specified on the DRAGEN command line. |