19188 run notes first draft

docs/run-notes/19188_run_notes.md

+# Trio whole exome - 19188 (EdGe)
+
+* Fam 435981 - urgent trio
+* Fam 404190, Individual 128589 is a repeat maternal sample - other 2 samples are from 14110_Ansari_Morad
+* Fam 433855, Individual 128681 is a repeat proband sample - other 2 samples are from 18610_Ansari_Morad
+* Fam 428986 affected duo, for shared variant analysis
+* Fam 435139 quad – similarly affected brothers. Shared & trio analysis.
+* Fam 434642 duo for Congenica
+* Fam 434889 duo for Congenica
+
+## QC notes
+
+**Note:** family 433924 had to be re-started and is not included in these notes yet.
+
+* All passed pedigree checks
+* Coverage a little low for:
+  * 128450_434883 - 35X - unaffected father
+  * 128360_434801 - 37X - proband
+  * 84873_435139 - 37X - proband
+  * 128102_429275 - 43X - unaffected father
+  * 128540_434918 - 43X - unaffected mother
+* Slight contamination for:
+  * 128540_434918 - 2.9% - unaffected mother (also with slightly low coverage 43X above)
+* Relatedness looks fine
+* All correct sex
+* 120967_434490 (male proband) has slightly odd X/Y mapping percentages at 80/20. Most males are in a tight range of 88-90%, it's a clear outlier.
+* 128102_429275 (unaffected father, also with slightly low coverage 43X above) has very odd chromosome mapping percentages and GC content distribution.
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