Convert COSMIC fusions to BEDPE format

rdocking / fusebench

A workbench for aggregation and interpretation of RNA-Seq gene fusions

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Convert COSMIC fusions to BEDPE format #39

Closed rdocking closed 6 years ago

rdocking commented 6 years ago

From the COSMIC db flat file of fusions, write a converter to convert to BEDPE format

rdocking commented 6 years ago

COSMIC fusion export is downloaded to:

/home/projects/hackseq17_3/annotation_sources/cosmic/CosmicFusionExport.tsv

stefpiatek commented 6 years ago

happy to take this after some food

rdocking commented 6 years ago

Thanks!

stefpiatek commented 6 years ago

Looking at the cosmic data, I can get the transcript so work out the chromosome from that. Some have HGVS from the transcript so I'll pick out the the genomic position for the start and end for them.

If they don't have a chromosome, g_start and g_end in both should I remove the fusion or keep eveything in?

rdocking commented 6 years ago

For now, we can omit them - it doesn't really make sense to keep them if we can't get a coordinate.