Snpeff-Reannotation

Question

[Maria]

Hello,

Any one know . What happens if we re annotate a annotated vcf?

Is it possible to re annotate a file and merge new annotation with previous annotation without over write the previous annotations

Answer 1

[Pablo]

For VCF files currently SnpEff will add another 'EFF' field in the INFO column. If you have suggestions on what the default behaviour should be, I'm open to change this for the next release.

[Rlong]

It would be helpful if annotations happened in the per-sample genotype fields. If the tags are in the INFO column, they can only apply to a single sample, and not multiple variants found in possibly many samples across a population group at the same position.

[Pablo]

I don't think this is the way VCF was designed, but may be I misunderstood your comment... The INFO fields applies to all samples. You simple need to use the GT field to discriminate which one the EFF applies to. Does this make sense?