[ensembl-dev] vep --pick option

[Allison Regier]

I noticed that with the --pick option, vep will only annotate one alternate allele if there are multiple alternates in the vcf entry.  This seems undesirable - is it intended?
For example, a variant at 
21      39207700        .       T       C,G

got the annotation
CSQ=C|ENSG00000157542|ENST00000609713|Transcript|INTRONIC||||||||||||-1|YES|KCNJ6|HGNC|||ENST00000609713.1:c.25+5260A>G|
with --pick turned on

and
CSQ=C|ENSG00000157542|ENST00000288309|Transcript|INTRONIC||||||||-1|KCNJ6|HGNC|,G|ENSG00000157542|ENST00000288309|Transcript|INTRONIC||||||||-1|KCNJ6|HGNC|,C|ENSG00000157542|ENST00000609713|Transcript|INTRONIC||||||||-1|KCNJ6|HGNC|,G|ENSG00000157542|ENST00000609713|Transcript|INTRONIC||||||||-1|KCNJ6|HGNC|
with --pick turned off

I would have liked to see the “top” transcript picked for each alternate allele:
CSQ=C|ENSG00000157542|ENST00000609713|Transcript|INTRONIC||||||||||||-1|YES|KCNJ6|HGNC|||ENST00000609713.1:c.25+5260A>G|,G|ENSG00000157542|ENST00000609713|Transcript|INTRONIC||||||||-1|KCNJ6|HGNC|
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