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** We have fixed the bug related to FILTER=GENOTYPED and FILTER=GENOTYPED_ONLY which was causing a crash in bcftools.
** We have fixed the bug related to FILTER=GENOTYPED and FILTER=GENOTYPED_ONLY which was causing a crash in bcftools.
* Removed --doseOutput and --hapOutput. Please use DosageConvertor to convert your files to dosage format.
* '''Obsolete Features'''
** In Minimac4, we removed the <code>--doseOutput</code> and <code>--hapOutput</code> options. Please use [[DosageConvertor |DosageConvertor]] to convert your files to MaCH or PLINK dosage format.
** Currently Minimac4 can ONLY handle M3VCF format files. If your reference panel is in VCF format, please use Minimac3 to convert the VCF file to M3VCF (along with parameter estimation) and then use that M3VCF for imputation using Minimac4. The same holds for the option <code>--processReference</code> as well. Although the handle is made available, we will implement it in a later version.
** Parameters such as <code>--rounds</code>, <code>--states</code>, <code>--rec</code>, <code>--err</code> have been deactivated for now until we implement parameter estimation in minimac4.
= Reference Panels for Download =
= Reference Panels for Download =
