Used in: gor only

VERIFYVARIANT

The VERIFYVARIANT command ensures that the reference column (REF or REFERENCE) corresponds to the reference from the configured build. It also verifies that the alt column (ALT, CALL or ALLELE) does not exceed a maximum length.

Usage

gor ... | VERIFYVARIANT

Options

-ref col	The column denoting the reference seq.
-alt col	The column denoting the alternate (alleles) seq.
-maxlen len	The maximum length allowed for the alternate seq.