Warning messages

[woodoo46]

Hi there,

I am assuming that we can ignore the warning messages like following:

warning: unknown impact "sv:intron" from csq "sv:intron|FMR1NB||protein_coding|+||" please report the variant at https://github.com/brentp/slivar/issues

Thanks!

George

[brentp]

Hi, thanks for reporting. What tool made those annotations?

[woodoo46]

slivar tsv

[brentp]

I mean what tool added sv:intron|FMR1NB||protein_coding|+|| to your VCF?

[woodoo46]

svpack in pacbio pipeline, I think. This is the explanation of the field.
##INFO=<ID=BCSQ,Number=.,Type=String,Description="Local consequence annotation. Format: Consequence|gene|transcript|biotype|strand|amino_acid_change|dna_change">