gvcftools 0.16

Human clinical applications require sequencing information for both variant and non-variant positions, yet there is currently no common exchange format for such data. Genome VCF (gVCF) was developed to address this issue. gVCF is a set of conventions applied to the standard variant call format (VCF). These conventions allow representation of genotype, annotation and other information across all sites in the genome in a reasonably compact format: typical human whole genome sequencing results expressed in gVCF with annotation are less than 1 Gbyte, or about 1/100 the size of the BAM file used for variant calling. gVCF is also equally appropriate to represent and compress targeted sequencing results. Compression is achieved by joining contiguous non-variant regions with similar properties into single ‘block’ VCF records. To maximize the utility of gVCF, especially for high stringency applications, the properties of the compressed blocks are conservative -- thus block properties like depth and genotype quality reflect the minimum of any site in the block. The gVCF file is also a valid VCF v4.1 file, thus it can be indexed and used with existing VCF tools such as tabix and IGV, making it convenient both for direct interpretation and as a starting point for tertiary analysis.

Accessing the software

To load the module:

$ module load apps/gvcftools/0.16

gvcftools has a collection of binaries that can be found at ${GVCFTOOLS_ROOT}.

Accessing Previous Versions

Wherever possible, previous versions of this application will be retained for continuity, especially for research projects that require a consistent version of the software throughout the project. Such versions, however, may be unsupported by IT Services or the applications vendor, and may be withdrawn at short or no notice if they can no longer run on the cluster - for example, essential operating system upgrades may be incompatible with old versions.

At present there are no previous versions of this application on the BlueBEAR service.

Known Problems & Limitations


Other Information

The Support Level for this application is An.

Visit the gvcftools website for more information regarding this application.

Last modified: 11 September 2017