Feature request: joint somatic DNA + RNA mode

Illumina / manta

Structural variant and indel caller for mapped sequencing data

GNU General Public License v3.0

404 stars 154 forks source link

Feature request: joint somatic DNA + RNA mode #192

Open iskandr opened 5 years ago

iskandr commented 5 years ago

I often have normal WES, tumor WES, and tumor RNA and would like to call somatic variants in the tumor RNA and filter them by (1) evidence in tumor DNA and (2) lack of evidence in normal DNA.

ctsa commented 5 years ago

Thanks, unfortunately joint DNA/RNA analysis has been a recurring feature request which we haven't been able to meet. There is work on SV genotyping from VCF which might partially enable this workflow by allowing you to take the output from an RNA analysis and then genotype it in T/N mode as an additional filter. As I can't give a solid timeline on that feature, you might be able to create a similar workflow today using Delly genotyper?