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MQ0Fraction, HWP, Dels Tags for VCF file (How to generate)
My issue might be very fundamental. I am looking for the values for the tags mentioned in the title after running variantAnnotator on the VCF file. However, they were mentioned in the header section but not included elsewhere. I need these tags for variant filtering.
This is the code that I have used:
java -Xmx6g -jar $GATK -R $REF -T VariantAnnotator -V h3_variant.vcf -o VA_h3_variant.vcf -A HardyWeinberg -A HomopolymerRun -A MappingQualityZero -A SpanningDeletions
There is no error/warning given.
I wonder if there are any alternatives to these statistics?