STARconsensus: mapping RNA-seq reads to consensus genome.

• Introduced in STAR 2.7.7a (2020/12/28)

• Provide the VCF file with consensus SNVs and InDels at the genome generation stage with --genomeTransformVCF Variants.vcf --genomeTransformType Haploid. The alternative alleles in this VCF will be inserted to the reference genome to create a “transformed” genome. Both the genome sequence and transcript/gene annotations are transformed.

• At the mapping stage, the reads will be mapped to the tranformed (consensus) genome. The quantification in the transformed annotations can be performed with standard --quantMode TranscriptomeSAM and/or GeneCounts options. If desired, alignments (SAM/BAM) and spliced junctions (SJ.out.tab) can be transformed back to the original (reference) coordinates with --genomeTransformOutput SAM and/or SJ. This is useful if downstream processing relies on reference coordinates.