Open ptn24 opened 5 years ago
this is an oversight and therefore a deficiency in vcfanno, but it doesn't make sense to use by_alt
on a bed file (where you don't have ref
and alt
columns to indicate the exact allele).
That makes sense. If the INFO tag is for the whole locus though, then would it be possible to make the metadata line for INFO/ENCFF171LNJ say Number=.
(cf. https://samtools.github.io/hts-specs/VCFv4.2.pdf)? It could also be useful to add a line to the documentation and/or print a warning to stdout about BED annotations (just a thought)
Alternatively, what do you think about duplicating the annotations across ALT alleles when users pass in by_alt
+ BEDs? Not ideal, but users would have control
i think it should probably be an error to use by_alt with a file that doesn't have ref, alt. why don't you use op of concat
?
Good suggestion, will do
The
by_alt
operation should use pipes (perhaps this could be parameterized) to delimit multiple annotations for a single ALT allele. However when adding BED annotations, vcfanno seems to use commas to delimit annotationsExpected
INFO
to equalENCFF171LNJ=28|20.0
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