Joint Variant Calling

Avocado’s Jointer command supports joint variant calling from gVCF-styled data. The Jointer command can also be used to export Apache Parquet Genotype data to VCF, and to joint genotype a collection of samples who all scored the same set of variants. Our joint variant calling approach is is described in Chapter 7 of this thesis.

To run the Jointer command, you must provide two parameters:

• The path to all input files to joint genotyping (to load multiple files, use Hadoop’s glob syntax.
• The path to save the output to, as a VCF file.

To save the VCF file as a single file (instead of sharded output), pass the -single flag.

If run on a single sample, Jointer will calculate variant statistics (VCF INFO column attributes) and qualities only. If run on multiple samples, the Jointer command will update the called genotypes using a binomial prior that is informed by the observed allele frequency of the variant across all samples with confident calls. If the input data for the multiple samples is in gVCF format, pass the -from_gvcf flag.