Outputs¶

gNALI's output directory contains the following items:

Item	Type	Description
Basic output	txt file	Status of all input genes.
Detailed output	txt file	Variants of input genes passing filtering with some annotations extracted.
VCF output	vcf file	(Optional) Variants of input genes passing filtering as a VCF.

Basic output¶

All input genes will be flagged with one of the following:

• HC LoF found: gene has high-confidence loss-of-function variants that also pass any custom filtering specified
• HC LoF found, failed filtering: gene has high-confidence loss-of-function variants but no variants pass custom filtering specified
• Unknown gene: gene was not found in the Ensembl homo sapiens database. This is usually caused by using gene aliases, non-HGNC formats, or non-human genes in the input file
• No variant found in database: no variants were found for an input gene using the database specified
• No HC LoF found: gene does not have known high-confidence loss-of-function variants

Detailed output¶

Contains loss-of-function variants passing filtering with some annotations extracted (and optionally population frequency data).

VCF output¶

This output is created if the --vcf flag was used. Contains headers and variant records of input genes passing filtering.