Annotate Files (Standalone Nirvana Tool)

If you have not generated a VCF file, download a VCF file using the following command

curl -O https://raw.githubusercontent.com/HelixGrind/DotNetMisc/master/TestFiles/HiSeq.10000.vcf.gz

IAE supports uncompressed VCF files and bgzip compressed VCF files. VCF files that have been compressed by standard gzip are not supported.

To annotate the file, enter the following command:

/opt/edico/share/nirvana/Nirvana -c ~/Data/Cache/GRCh38/Both \ -r ~/Data/References/Homo_sapiens.GRCh38.Nirvana.dat \ --sd ~/Data/SupplementaryAnnotation/GRCh38 -i HiSeq.10000.vcf.gz -o HiSeq.10000

The following are the available command line options:

Option	Value	Example	Description
-c	Directory	~/Data/Cache/GRCh38/Both	Cache directory
-r	Directory	~/Data/References/Homo_sapiens.GRCh38.Nirvana.dat	Reference directory
--sd	Directory	~/Data/SupplementaryAnnotation/GRCh38	Supplementary annotation directory
-i	path	HiSeq.10000.vcf.gz	Input VCF path
-o	prefix	HiSeq.10000	Output path prefix

Using the example above, IAE generates the following output called HiSeq.10000.json.gz.

---------------------------------------------------------------------------

Stromberg, Roy, Lajugie, Jiang, Li, and Kang 3.9.1-0-gc823805

---------------------------------------------------------------------------

Initialization Time Positions/s

---------------------------------------------------------------------------

Cache 00:00:01.9

SA Position Scan 00:00:00.4 23,867

Reference Preload Annotation Variants/s

---------------------------------------------------------------------------

chr1 00:00:00.4 00:00:03.7 2,651

Summary Time Percent

---------------------------------------------------------------------------

Initialization 00:00:02.3 25.7 %

Preload 00:00:00.4 5.4 %

Annotation 00:00:03.7 41.5 %

Peak memory usage: 1.284 GB

Time: 00:00:08.0