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?
Thanks very much for your in-depth insight and helpful comment. I never heard of Manta and I will give it a try. Regarding the panel, we used SureSelect all Exon v5. PanelApp will definitely be useful in the future.
Once more, thank you for your time to help me with this.