RNA Variant Calling

DRAGEN RNA variant calling uses the DRAGEN Somatic Small Variant Caller to call SNVs and indels. DRAGEN uses somatic variant calling to account for nongermline variant allele frequencies in RNA-Seq data caused by differential expression. To perform variant calling, DRAGEN uses a probability model that weighs the evidence of a real variant against evidence for various noise models. If the quality score for a variant exceeds a certain threshold, then the variant is reported in the output VCF with the PASS label. DRAGEN also applies filters, such as weak_evidence and base_quality, that might indicate if the variant does not reach the thresholds required to qualify as a passing call. For more information on DRAGEN DNA somatic variant calling, see Somatic Mode.

You can also use force genotyping (ForceGT) with RNA variant calling. You can input a VCF that contains variants of interest, and the output VCF will contain all variants from the input with annotation. ForceGT might be unable to accurately call complex variants or variants with long deletions (> 50 bp). Complex variants are variants that require more than one substitution, insertion, or deletion event to transform the REF allele into the ALT allele.