bcftools split vep miss variant without allele frequency when using -f to print gnom_af

[liuhankui]

bcftools +split-vep vep.vcf -s worst -f "%CHROM %POS %REF %ALT\n"

chr18 12312939 G C
chr18 12312971 C T
chr18 12314310 G C

bcftools +split-vep vep.vcf -s worst -f "%CHROM %POS %REF %ALT %gnomADg_AF\n"

chr18 12312939 G C 0.800479
chr18 12314310 G C 0.790057

---

miss chr18 12312971

[pd3]

I updated the documentation to emphasize that unlike bcftools query -f, the plugin bcftools +split-vep -f drops lines where all queried VEP fields are empty.

Assuming you are using a recent version of the plugin (1.18+), you can change this behavior by providing the option -X, --keep-sites.

-x, --drop-sites      Drop sites without consequences after -s is applied (the default with -f)
-X, --keep-sites      Do not drop sites without consequences (the default without -f)

I hope this helps

[liuhankui]

-X, a nice option, thanks a lot!