v1.3

This latest release removes built-in functional variant annotation. However, users can still perform functional variant annotation on the output .vcf.gz and .vcf.gz.tbi files for their sample of interest.

Importantly, this release adds annotation of high-risk human aligned mouse alleles (HAMAs) described in Jo et al (2019). This feature builds upon the existing specialization of this pipeline for tumor-only short somatic variant calling for PDX models.

v1.2

Added nextflow modules

v1.1

Automatic downloading of accessory files