Convert NCBI Downloaded files to ANNOVAR format
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12 weeks ago
robert • 0

I have been trying to understand from the ANNOVAR documentation and other sites the steps needed to make these files from NCBI available to ANNOVAR. I admit to being new to bioinformatics, but have been a software developer for 30+ years. My goal is to annotate by hg38 based VCF file but do not even have a lead as to what to do with the downloaded files. From what I can tell, convert2annovar doesn't support these.

I downloaded because all of the files on the ANNOVAR download site are almost a year old and I am trying to help determine the gene(s) for a genetic condition for which the genes are not yet known - so the latest and greatest information seemed appropriate.

  • GCF_000001405.40_GRCh38.p14_genomic.fna
  • genomic.gff
  • protein.faa
  • genomic.gtf
  • rna.fna
  • cds_from_genomic.fna

Thanks for any help. References to other resources would be most welcome. I am happy to learn, but have come up empty using web searches.

ANNOVAR • 346 views
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The documentation is clear on this: convert2annovar.pl is used to convert input (genotype) files to ANNOVAR format. It is not used on dictionary files or annotation sources

Do you absolutely need to use ANNOVAR? For best results, I recommend using VEP.

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Ok I guess I got confused because there is support for, for example gff3-solid, but not directly gff files. I will have a look at VEP, but the issue may simply be that I am not familiar enough with the files, purposes and formats. Thank you

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You may also find tools such as vcfanno and bcftools easier to work with, if you don't want to spend too much time reformatting dictionary files.

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