Here I've got a patient with an unidentified neurodevelopmental complication and primary WES analysis with candidate gene approach resulted in no significant finding. I understand that the causative mutation may reside in an intronic region, but the patient underwent good-old Karyotyping in 1999 and a balanced translocation was identified.
I was wondering if there's any practical approach to identify splitted reads at the position of translocation. I guess this could be done by investigating
MRNM field in the SAM file, but is there any software that streamlines this?