DR12 - DR11 follow-ups

[edsu7]

P1000-US contamination:

donorId	sampleId	normal_mutect2_contamination	tumour_mutect2_contamination	notes
DO253906	SA617093	0.06756965	0.22054257	Marked in DR9;M:SA617093 normal contamination >0.04;M:SA617094 tumour contamination >0.04;S: SA617093 vs SA617094 not called;P: SA617093 vs SA617094 missing variant calls;SA617093 vs SA617094 only has unreleased files
DO253972	SA617191	0.00883971	0.04169197	Marked in DR9;M:SA617239 tumour contamination >0.04;S: SA617191 vs SA617239 not called;P: SA617191 vs SA617239 missing variant calls;SA617191 vs SA617239 only has unreleased files
DO253979	SA617262	0.0685698	0.08156983	Marked in DR9;M:SA617262 normal contamination >0.04;M:SA617263 tumour contamination >0.04;S: SA617262 vs SA617263 not called;P: SA617262 vs SA617263 missing variant calls;SA617262 vs SA617263 only has unreleased files
DO253912	SA617056	0.05583455	0.09779626	Marked in DR9;M:SA617056 normal contamination >0.04;M:SA617088 tumour contamination >0.04;S: SA617056 vs SA617088 not called;P: SA617056 vs SA617088 missing variant calls;SA617056 vs SA617088 only has unreleased files
DO253968	SA617230	0.04333199	0.10280027	Marked in DR9;M:SA617230 normal contamination >0.04;M:SA617218 tumour contamination >0.04;S: SA617230 vs SA617218 not called;P: SA617230 vs SA617218 missing variant calls;SA617230 vs SA617218 only has unreleased files
DO253955	SA617224	0.03176104	0.05894849	Marked in DR9;M:SA617211 tumour contamination >0.04;S: SA617224 vs SA617211 not called;P: SA617224 vs SA617211 missing variant calls;SA617224 vs SA617211 only has unreleased files

RNA issues:

analysisId	sampleId	PIPELINE	mapping_pct	pct_coding_bases	pct_intergenic	pct_intronic	notes
45d6bec3-a70f-4c16-96be-c3a70fac1606	SA616950	STAR	51.14	0.308635	0.175019	0.151195	;coverage exceeds 120M;mapping under 80%;pct coding bases <35%
cd798492-13a3-4cae-b984-9213a3fcae77	SA616950	HISAT2	4.45	0.323847	0.165045	0.144544	;mapping under 80%;pct coding bases <35%
351f66e5-8eb0-4f71-9f66-e58eb0bf71ab	SA616959	HISAT2	16.29	0.358127	0.148325	0.061579	;mapping under 80%
5721af91-8952-4f6e-a1af-9189521f6e7a	SA616959	STAR	16.98	0.365682	0.145986	0.048427	;mapping under 80%
814ed6cb-b5ff-48b3-8ed6-cbb5ff28b3dd	SA616963	HISAT2	-4.72	0.371272	0.15202	0.097686	;mapping under 80%
c76f5787-9e50-4893-af57-879e505893ad	SA616963	STAR	48.95	0.346147	0.166994	0.111389	;coverage exceeds 120M;mapping under 80%;pct coding bases <35%
d3207167-8c36-463b-a071-678c36663b19	SA617924	HISAT2	83.05	0.119782	0.164896	0.56071	;dup_percent under 30%;pct coding bases <35%;total intergenic and intronic >40%
ff11d712-b696-4370-91d7-12b6962370a3	SA617924	STAR	94.98	0.11977	0.161414	0.564398	;coverage exceeds 120M;dup_percent under 30%;pct coding bases <35%;total intergenic and intronic >40%
3e82f86d-6485-4a77-82f8-6d64859a7708	SA617939	STAR	88.5	0.11484	0.178774	0.55231	;pct coding bases <35%;total intergenic and intronic >40%
9ea1ec2d-9253-473b-a1ec-2d9253473bb3	SA617939	HISAT2	78.72	0.114098	0.185829	0.541163	;mapping under 80%;pct coding bases <35%;total intergenic and intronic >40%
bf0271e9-5c9e-4774-8271-e95c9e0774fb	SA617964	STAR	91.4	0.112556	0.146549	0.596473	;coverage exceeds 120M;pct coding bases <35%;total intergenic and intronic >40%
f2d1eb23-bb61-4bbb-91eb-23bb614bbbb5	SA617964	HISAT2	82.26	0.112003	0.151259	0.588546	;coverage exceeds 120M;pct coding bases <35%;total intergenic and intronic >40%
6e98617d-7a08-463a-9861-7d7a08b63a18	SA617985	HISAT2	96.85	0.195622	0.604443	0.014092	;coverage exceeds 120M;pct coding bases <35%;total intergenic and intronic >40%
958faa74-89f6-40a0-8faa-7489f610a082	SA617985	STAR	98.43	0.194629	0.603594	0.01627	;coverage exceeds 120M;pct coding bases <35%;total intergenic and intronic >40%
83e02b4c-9d73-43d5-a02b-4c9d7343d5fe	SA618002	HISAT2	96.09	0.193728	0.119573	0.522267	;coverage exceeds 120M;dup_percent under 30%;pct coding bases <35%;total intergenic and intronic >40%
9be951c7-3f1d-426e-a951-c73f1d026ea8	SA618002	STAR	98.07	0.193412	0.119608	0.523996	;coverage exceeds 120M;dup_percent under 30%;pct coding bases <35%;total intergenic and intronic >40%
a701dee1-b066-438e-81de-e1b066138edf	SA618061	STAR	81.56	0.018191	0.565991	0.222772	;coverage exceeds 120M;pct coding bases <35%;total intergenic and intronic >40%
ae8d7ba1-93f4-4597-8d7b-a193f435971b	SA618061	HISAT2	91	0.015985	0.548838	0.199316	;coverage exceeds 120M;pct coding bases <35%;total intergenic and intronic >40%
3942f9c4-5d0a-442a-82f9-c45d0a342ad5	SA618125	STAR	93.01	0.12258	0.221257	0.498323	;coverage exceeds 120M;pct coding bases <35%;total intergenic and intronic >40%
433b9336-59dd-4273-bb93-3659dde273db	SA618125	HISAT2	80.61	0.118378	0.234653	0.478835	;coverage exceeds 120M;pct coding bases <35%;total intergenic and intronic >40%