HarvestTools v1.3

New features

• VCF annotations - There are new INFO fields in VCF output indicating what CDS locus, if any, each variant lies in, the amino acid changes for each allele, and whether all alleles are synonymous.
• Internal variants - The --internal option for VCF export restricts to positions that differ within a group of genomes. The group can be specific track names or a clade, specified as the LCA of two tracks. Columns will be restricted to the genomes of interest.
• Signature variants - The --signature option for VCF export restricts to positions that are consistent within a group of genomes and different outside of it. The group can be specific track names or a clade, specified as the LCA of two tracks. All columns will be included.

Changes

• GenBank annotations are now reconciled with fasta reference sequences using accessions rather than GIs, due to the retirement of GIs by NCBI.