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Removing NON_REF tags from VCF
Dear GATK Team,
I ran HaplotypeCaller in GVCF mode and extracted variants using gvcftools "extract_variants". VCF has "NON_REF" tags which carried from g.vcf.
I want to generate both g.vcf & vcf for each sample. Instead of running haplotypecaller again for getting vcf, I am using gvcftools "extract_variants" to extract variants from existing g.vcf which is faster.
Please suggest me how can i get rid of NON_REF tags in vcf file.
Thanks In Advance