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Minor usage clarification
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pd3 committed Aug 22, 2021
1 parent 3647090 commit 7956618
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4 changes: 3 additions & 1 deletion plugins/split-vep.c
Original file line number Diff line number Diff line change
Expand Up @@ -195,7 +195,7 @@ static const char *usage_text(void)
" --columns-types -|FILE Pass \"-\" to print the default -c types or FILE to override the presets\n"
" -d, --duplicate Output per transcript/allele consequences on a new line rather rather than\n"
" as comma-separated fields on a single line\n"
" -f, --format STR Formatting expression for non-VCF/BCF output, same as `bcftools query -f`\n"
" -f, --format STR Create non-VCF output; similar to `bcftools query -f` but drops lines w/o consequence\n"
" -l, --list Parse the VCF header and list the annotation fields\n"
" -p, --annot-prefix STR Before doing anything else, prepend STR to all CSQ fields to avoid tag name conflicts\n"
" -s, --select TR:CSQ Select transcripts to extract by type and/or consequence severity. (See also -S and -x.)\n"
Expand Down Expand Up @@ -246,6 +246,8 @@ static const char *usage_text(void)
" # the -x switch. See the online documentation referenced above for more examples.\n"
" bcftools +split-vep -c gnomAD_AF:Float -s :missense file.vcf.gz\n"
" bcftools +split-vep -c gnomAD_AF:Float -s :missense -x file.vcf.gz\n"
"\n"
" See also http://samtools.github.io/bcftools/howtos/plugin.split-vep.html\n"
"\n";
}

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