Medaka tools annotation missing QUAL values
Hi
QUAL data is missing in the annotated vcf file.
medaka_haploid_variant reads.fasta ref.fasta -t 30
output : consensus_to_ref.vcf
It has no annotations. So I annotated the vcf
medaka tools annotate consensus_to_ref.vcf ref.fasta mapped-sorted.bam variants.annot.vcf
output: variants.annot.vcf
In this vcf, there is no information in the 'QUAL' column
Am I doing something wrong?
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Ram
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SUDOsundu •
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SUDOsundu •
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Hi. Did you figure this out? I have the same issue.
Not yet. I am trying medaka variants and filtering for haploid genome.
Can you share the code lines you are using to do this? Also did it work?