report_IBD.md

Report of IBD analysis stage of pre-QC

Report produced by J. Juodakis on 2015-06-15 15:55

Data obtained from files /home/julius/Desktop/2015MAR/all_arrays/MERGED_COMMON2.bed, /home/julius/Desktop/2015MAR/all_arrays/MERGED_COMMON2.bim, /home/julius/Desktop/2015MAR/all_arrays/MERGED_COMMON2.fam

IBD statistics obtained from ./pre-QC/ibd//home/julius/Desktop/2015MAR/all_arrays/MERGED_COMMON2_ibd-results.genome

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This is an additional report for the identity-by-descent analysis. The statistics provided here were generated using the .fam file that includes any adjustments following the pre-QC stage. This report will present any cases where IBD PI_HAT statistic deviates from the predictions, and will generate likely explanations for this deviation.

Data Files Being Used

In the .fam file used for this analysis, there are 365 unique families with 790 genotyped individuals (rows). There are 518 declared fathers (V3) and 518 mothers (V4), of which 321 and 316 are unique; 126 and 94 are actually genotyped in this dataset. In total there are 17 successfully genotyped full family trios. These declared relationships exist in the .fam file:

FS	HS	OT	PO	UN
243	3	108	278	311023

The IBD file has 311655 pairwise comparisons, 365 unique families and 790 unique individuals.

Pairwise PI_HAT value histogram split by type of declared relationship:

Agreement and Conflicts between the .fam file and genetics

Among the 278 declared Parent-Offspring pairs 0 problems were found (0 were genetically Unrelated, 0 Full Siblings, 0 Monozygotic Twins, 0 Half Siblings, 0 Unexplained, 0 explanations were overlapping).

Among the 311023 declared Unrelated pairs 16 problems (related pairs) were found (1 were genetically Parent-Offspring pairs, 0 Full Siblings, 0 Monozygotic Twins, 1 Half Siblings, 14 Unexplained, 0 explanations were overlapping).

Among the 243 declared Full Sibling pairs 3 problems were found (0 were genetically Unrelated pairs, 0 Parent-Offspring pairs, 1 Monozygotic Twins, 2 Half Siblings, 0 Unexplained, 0 explanations were overlapping).

Among the 108 declared Other-Type relationship pairs 40 were genetically Unrelated, 2 were Parent-Offspring pairs, 0 were Full Siblings, 0 Monozygotic Twins, 63 Half Siblings, 3 Unexplained, 0 explanations were overlapping.

Please note that for downstream procedures (phasing and imputation) only Parent-offspring problems must be solved now. However, it is very important to take into account the violation of sample independence assumption in the GWAS analysis following QC/phasing/imputation: "other-type" relationships in this report ideally should be genetically unrelated, but it actually is not, thus exclusion step is required.

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Detailed list of explained conflicts

Declared as Parent-Offspring

Unrelated:

Full siblings:

Half siblings:

Monozygotic twins:

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Declared as Full-Sibling

Unrelated:

Parent-Offspring:

Half siblings:

	FID1	IID1	FID2	IID2	Z0	Z1	Z2
158475	106	106	106	106_1	0.53	0.47	0.00
276411	244	244_1	244	244_2	0.55	0.45	0.00

Monozygotic twins:

	FID1	IID1	FID2	IID2	Z0	Z1	Z2
24753	15	15	15	15_1	0.00	0.00	1.00

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Declared as Other-Type

Unrelated:

	FID1	IID1	FID2	IID2	Z0	Z1	Z2
32281	20	20	20	20_4	0.72	0.28	0.00
32282	20	20	20	20_4_1	0.87	0.12	0.01
32283	20	20	20	20_4_2	0.85	0.14	0.01
33026	20	20_1	20	20_3	0.97	0.03	0.00
33027	20	20_1	20	20_4	0.96	0.04	0.00
33028	20	20_1	20	20_4_1	1.00	0.00	0.00
33029	20	20_1	20	20_4_2	0.98	0.00	0.01
33772	20	20_2	20	20_4	0.74	0.26	0.00
33773	20	20_2	20	20_4_1	0.90	0.09	0.01
33774	20	20_2	20	20_4_2	0.89	0.09	0.02
34517	20	20_3	20	20_4_1	0.77	0.23	0.00
34518	20	20_3	20	20_4_2	0.77	0.23	0.00
68403	43	43_1	43	43_2	0.99	0.00	0.01
100081	62	62_1	62	62_2	0.97	0.03	0.00
105895	66	66_1	66	66_2	1.00	0.00	0.00
129550	83	83_1	83	83_2	0.91	0.09	0.00
132557	86	86	86	86_3_1	0.81	0.19	0.00
133154	86	86_1	86	86_3_1	0.88	0.12	0.00
133750	86	86_2	86	86_3_1	0.92	0.08	0.01
140252	90	90_1_1	90	90_2_1	0.81	0.19	0.00
161230	107	107_2_3	107	107_3	0.74	0.25	0.01
161231	107	107_2_3	107	107_4	0.71	0.29	0.00
166127	110	110_3	110	110_4_1	0.60	0.40	0.00
203311	143	143_1	143	143_2	1.00	0.00	0.00
216390	156	156_1	156	156_2	1.00	0.00	0.00
233053	177	177	177	177_1_3	0.61	0.39	0.00
249528	195	195_1	195	195_2	0.99	0.00	0.01
274800	242	242_1	242	242_2	0.65	0.34	0.01
275610	243	243_1	243	243_2	0.98	0.02	0.00
277203	245	245_1	245	245_2	0.99	0.00	0.00
284395	259	259_1_1	259	259_2	0.70	0.30	0.00
286005	264	264_1	264	264_2	0.99	0.00	0.01
292741	283	283_1	283	283_2	1.00	0.00	0.00
293701	285	285_1	285	285_2	0.99	0.00	0.01
304516	321	321_1	321	321_2	0.97	0.03	0.00
307096	333	333_1	333	333_2	0.99	0.01	0.00
310116	357	357_1	357	357_2	0.99	0.00	0.00
311466	810	810	810	810_1	0.73	0.27	0.00
311485	810	810_1	810	810_2	0.70	0.30	0.00
311655	SAKNAS	254_1	SAKNAS	33551	0.98	0.02	0.00

Parent-Offspring:

	FID1	IID1	FID2	IID2	Z0	Z1	Z2
124690	80	80	80	80_1	0.00	1.00	0.00
235020	178	178	178	178_1	0.00	1.00	0.00

Full siblings:

Half siblings: (note that true uncles and aunts will also be listed here)

	FID1	IID1	FID2	IID2	Z0	Z1	Z2
790	1	1_1	1	1_2	0.54	0.46	0.00
5503	3	3_1	3	3_2	0.41	0.59	0.00
14050	7	7_1	7	7_2	0.51	0.49	0.00
34516	20	20_3	20	20_4	0.51	0.49	0.00
42645	24	24_1	24	24_2	0.53	0.47	0.01
48482	32	32_2	32	32_4	0.50	0.50	0.00
49206	32	32_3	32	32_4	0.51	0.49	0.00
56403	37	37	37	37_3	0.53	0.47	0.00
57116	37	37_1	37	37_3	0.53	0.47	0.00
59961	38	38_1	38	38_2	0.59	0.41	0.00
72570	45	45_1	45	45_2	0.44	0.56	0.00
84855	52	52_1	52	52_2	0.50	0.50	0.00
89545	55	55_1	55	55_2	0.54	0.46	0.00
94845	58	58_1	58	58_2	0.52	0.47	0.01
139079	90	90	90	90_1_1	0.46	0.54	0.00
139667	90	90_1	90	90_2_1	0.49	0.51	0.00
140251	90	90_1_1	90	90_2	0.53	0.47	0.00
140253	90	90_1_1	90	90_3	0.44	0.55	0.01
150060	98	98_1	98	98_2	0.57	0.42	0.00
159582	107	107	107	107_2_3	0.48	0.50	0.01
160132	107	107_1	107	107_2_3	0.49	0.51	0.00
160133	107	107_1	107	107_3	0.51	0.49	0.00
160134	107	107_1	107	107_4	0.53	0.47	0.00
160682	107	107_2	107	107_3	0.52	0.48	0.00
160683	107	107_2	107	107_4	0.52	0.48	0.00
164508	110	110	110	110_4_2	0.58	0.41	0.01
165048	110	110_1	110	110_4_1	0.46	0.54	0.00
165049	110	110_1	110	110_4_2	0.53	0.47	0.00
165588	110	110_2	110	110_4_1	0.56	0.44	0.00
165589	110	110_2	110	110_4_2	0.59	0.41	0.00
166128	110	110_3	110	110_4_2	0.60	0.40	0.00
167204	110	110_4_1	110	110_5	0.52	0.48	0.00
167740	110	110_4_2	110	110_5	0.54	0.46	0.00
169345	111	111_1	111	111_2	0.47	0.53	0.00
199081	138	138_1	138	138_2	0.52	0.47	0.00
210631	151	151_1	151	151_2	0.48	0.52	0.00
212866	153	153_1	153	153_2	0.48	0.51	0.01
215076	155	155_1	155	155_2	0.46	0.54	0.01
219850	159	159_1	159	159_2	0.47	0.51	0.02
221133	160	160_1	160	160_5	0.52	0.47	0.01
221134	160	160_1	160	160_6	0.46	0.54	0.00
221557	160	160_2	160	160_5	0.60	0.40	0.00
221558	160	160_2	160	160_6	0.58	0.42	0.00
221980	160	160_3	160	160_5	0.56	0.43	0.01
221981	160	160_3	160	160_6	0.56	0.44	0.00
230250	174	174_1	174	174_2	0.45	0.55	0.00
231456	175	175_1	175	175_2	0.45	0.55	0.00
233052	177	177	177	177_1_2	0.57	0.43	0.00
233841	177	177_1_1	177	177_1_2	0.49	0.51	0.00
233842	177	177_1_1	177	177_1_3	0.48	0.52	0.00
243760	189	189_1	189	189_2	0.41	0.58	0.01
255711	203	203_1	203	203_2	0.46	0.53	0.01
271186	234	234_1	234	234_2	0.46	0.53	0.01
283927	259	259	259	259_1_1	0.46	0.54	0.00
284162	259	259_1	259	259_2	0.42	0.58	0.01
303528	317	317_1	317	317_2	0.55	0.44	0.01
304517	321	321_1	321	321_3	0.54	0.46	0.00
304635	321	321_2	321	321_3	0.44	0.56	0.00
305554	326	326_1	326	326_5	0.43	0.56	0.01
305663	326	326_2	326	326_5	0.52	0.47	0.01
305771	326	326_3	326	326_5	0.52	0.48	0.01
305878	326	326_4	326	326_5	0.48	0.52	0.00
311095	603	603_1	603	603_2	0.55	0.45	0.00

Monozygotic twins:

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Declared as Unrelated

Parent-Offspring:

	FID1	IID1	FID2	IID2	Z0	Z1	Z2
282251	254	254	SAKNAS	254_1	0.00	0.99	0.01

Full siblings:

Half siblings: (note that true uncles and aunts will also be listed here)

	FID1	IID1	FID2	IID2	Z0	Z1	Z2
286075	264	264_1	303	303	0.44	0.56	0.00

Monozygotic twins:

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Details about unexplained conflicts

Unresolved conflicts among Parent-Offspring pairs:

[1] "...none..."

Unresolved conflicts among Unrelated pairs:

	FID1	IID1	FID2	IID2	Z0	Z1	Z2
23009	14	14	264	264_1	0.76	0.24	0.00
23080	14	14	303	303	0.75	0.25	0.00
23768	14	14_1	264	264_1	0.79	0.21	0.00
23839	14	14_1	303	303	0.78	0.22	0.00
24526	14	14_2	264	264_1	0.76	0.24	0.00
24597	14	14_2	303	303	0.76	0.24	0.00
113188	72	72_2	204	204	0.74	0.26	0.00
210106	150	150_1	345	345	0.70	0.30	0.00
210107	150	150_1	345	345_1	0.72	0.28	0.00
225343	164	164	172	172	0.66	0.34	0.00
225344	164	164	172	172_1	0.79	0.21	0.00
285849	264	264	303	303	0.78	0.21	0.01
286076	264	264_1	303	303_1	0.71	0.28	0.01
311647	31840	31840	43810	43810	0.18	0.52	0.30

Unresolved conflicts among Full Sibling pairs:

[1] "...none..."

Unresolved conflicts among Other-Type pairs:

	FID1	IID1	FID2	IID2	Z0	Z1	Z2
139081	90	90	90	90_2_1	0.35	0.65	0.00
141420	90	90_2_1	90	90_3	0.40	0.60	0.00
164507	110	110	110	110_4_1	0.59	0.39	0.02