Check EGFR variant not getting called

[Ott-Alexander]

• try calling with Varscan
  -> only calls the insertion but not the deletion....
• 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".
• remap with dragen and bwa without indel realignment?
  -> reads are mapped differently with two DELs (13b and 2b) and a SNV (T>G)
• 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...
• 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