Check EGFR variant not getting called

[Ott-Alexander]

• [x] try calling with Varscan -> only calls the insertion but not the deletion....
• [x] dragen + evidence BAM -> not conclusive, only part of the region covered in evidence BAM. Seems to suggest that the reads can be realigned so that this variant "isn't needed".
• [x] remap with dragen and bwa without indel realignment? -> reads are mapped differently with two DELs (13b and 2b) and a SNV (T>G)
• [x] check position with Sanger sequencing to verfy variant? (aksed Sorin) -> variant known in literature as real and "not callable" in the Patho they call it by hand...
• [x] test with freebase mosaic calling (vc_mosaic.php) -> was called with vc_mosaic !

[Ott-Alexander]

• [ ] test mosaic calling on all tumor exomes
• [ ] check missed tumor variants vs. artifacts/germline