Medaka tools annotation missing QUAL values

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4.3 years ago

SUDOsundu ▴ 80

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?

haploid medaka variant-calling nanopore • 1.6k views

ADD COMMENT • link updated 19 months ago by Ram 45k • written 4.3 years ago by SUDOsundu ▴ 80

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Hi. Did you figure this out? I have the same issue.

ADD REPLY • link 4.2 years ago by jpn • 0

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Not yet. I am trying medaka variants and filtering for haploid genome.

ADD REPLY • link 4.2 years ago by SUDOsundu ▴ 80

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Can you share the code lines you are using to do this? Also did it work?

ADD REPLY • link 4.2 years ago by jpn • 0

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