search

samtools / bcftools

This is the official development repository for BCFtools. See installation instructions and other documentation here http://samtools.github.io/bcftools/howtos/install.html
http://samtools.github.io/bcftools/
Other
634 stars 241 forks source link

DIfference between "Absent", "Missing" and "Deletion" in bcftool consensus #2134

Closed Nagaemory closed 3 months ago

Nagaemory commented 3 months ago

Hi all,

I would like to know what are the options actually means and difference among them in bcftool consensus parameters

Absent (--a) Missing (--M) Deletion (-mark-del)

Thanks

pd3 commented 3 months ago

Mmmm, it is disappointing if the usage page is not clear enough

-a, --absent CHAR              Replace positions absent from VCF with CHAR
-M, --missing CHAR             Output CHAR instead of skipping a missing genotype "./."
    --mark-del CHAR            Instead of removing sequence, insert character CHAR for deletions

Absent from VCF = the position is not present in the VCF Missing genotype = the genotype is set to missing ("." or "./."). Deletion = REF allele is longer than ALT allele, for example REF=CTT and ALT=C

Please read the VCF specification https://samtools.github.io/hts-specs/VCFv4.3.pdf

If you can suggest a better wording to make this clearer, please let us know