Really cool software! Thanks for developing & maintaining it!
The guideline makes it clear strelka2 can be used for germline variant calling on RNA-seq data with the --rna flag. However, is it going to work fine with the somatic variant workflow too (e.g. tumor + normal pairs of RNAseq)?
RNA-Seq
The germline workflow can be configured with the --rna flag.
This will provide experimental settings for RNA-Seq variant calling.
At present this flag disables all high depth filters which are designed
to exclude pericentromeric reference compressions in the WGS case
but cannot be applied correctly to RNA-Seq analysis.
In addition the expected allele frequency of heterozygous variants
is expanded to account for allele specific expression and a custom
RNA-Seq empirical scoring model is used.
Really cool software! Thanks for developing & maintaining it!
The guideline makes it clear strelka2 can be used for germline variant calling on RNA-seq data with the
--rnaflag. However, is it going to work fine with the somatic variant workflow too (e.g. tumor + normal pairs of RNAseq)?https://github.com/Illumina/strelka/blob/v2.9.x/docs/userGuide/README.md#rna-seq