RNA Fusions: Genomic Validation of Fusions

[snasser]

Add genomic validation to Phoenix. The plan is to run genomicValidator on star.preliminary parallel to star fusionFilter/Annotator. Tasks: -Test Genomic validation on star preliminary (Sara N) -Add wrapper to convert Star results to Genomic Validation input format -Add/update files for Build38 --Update Process*.py script to read the b38 ENSG refflat --Update Process.py script to read the b38 Hugo refflat (RefSeq) --Update Process_.py has hard coded IG start -stop. This should be modified to read from a file which is build specific. -Identify all combinations of Genome/RNA for fusionValidator -Integrated Star final with genomic validator

-Use ensembl 98 for all testing not gencode31 (SN)

• Regenerate Immunoglibin Text file for collapsing (Ensembl V 98) use loci bed ( /home/tgenref/homo_sapiens/grch38_hg38/hg38tgen/tool_resources/tgen_lymphocyteReceptor_counts/lymphocyteReceptor_loci.bed for chr 14, 2, 22). --Keep same format as before

Add a bed file for a specific IGJ_DH, JH, etc...to the regions extracted from the new GTF.

[snasser]

@PedalheadPHX Replacing build37 Ig locations with these in genomicValidator. /home/tgenref/homo_sapiens/grch38_hg38/hg38tgen/tool_resources/tgen_lymphocyteReceptor_counts/lymphocyteReceptor_loci.bed

[snasser]

@awchrist We might need to save some preliminary star-fusion files for fusionValidator