Simple way to have VariantsToTable output all fields. Just want the entire VCF as a table.

[abalter]

I'm trying, for example,

gatk VariantsToTable -V clinvar.vcf -O clinvar.tsv

It goes through the motions and displays progress. The output file is created, and it has the right number of lines. But the lines are all empty!

Maybe add a default value to the -F switch?

[droazen]

@abalter Having -F default to all the fields in the VCF is a good suggestion -- the current behavior is definitely not intuitive.

[abalter]

@droazen -- is there a way to simply list all the possible fields in the header? Then I could use that list to create an input for the -F flag.

[droazen]

@abalter The complete list of fields should be present in the VCF header, but unfortunately I don't know of a convenient way to extract them apart from the manual method. It would be pretty simple to write a script or GATK tool to parse the VCF header and list all the fields, but the best solution would be to patch the VariantToTable to default -F to all the fields, as discussed above.

[slagelwa]

@abalter The complete list of fields should be present in the VCF header

Key word here is "should be", which isn't always the case.