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clintval / vartovcf

Convert variants from VarDict/VarDictJava into VCF v4.2 format.
MIT License
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Ensure VCFs are completely free of warnings from popular validators #54

Closed clintval closed 3 years ago

clintval commented 3 years ago

Right now, GATK doesn't like my genotype calling:

WARN  00:22:43,865 ValidateVariants - ***** one or more of the ALT allele(s) for the record at position chr1:114713880 are not observed at all in the sample genotypes *****
WARN  00:22:43,866 ValidateVariants - ***** one or more of the ALT allele(s) for the record at position chr1:114713883 are not observed at all in the sample genotypes *****
WARN  00:22:43,866 ValidateVariants - ***** one or more of the ALT allele(s) for the record at position chr1:114713883 are not observed at all in the sample genotypes *****