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HaplotypeCaller MappingQualityZero always is 0
I am using the standard HaplotypeCaller/GenotypeGVCFs pipeline with the --includeNonVariantSites option.
I always get MQ0=0 for all SNPs and don't get it reported for non-variants, even if I add "--annotation MappingQualityZero" to both commands.
With UnifiedGenotyper, MQ0 values are reported correctly.
Is this a bug?
Also, with HaplotypeCaller, MQ is only reported for variants, not for non-variants. Is there a way to get this annotation reported for non-variants, such as with UnifiedGenotpyer?
I am using Version 3.3-0, but collegues have a similar problem with version 3.2-2.