A.2.3. Variant calling

For each VCF file, several statistical indicators about variant calling were calculated from VARIANT:

run: 4 runs were performed for this study. Run 1 included all 11 controls: patients with known mutations.
sampleID: ID for each sample.
N. variants: total number for each patient.
N. biallelic: total number of biallelic variants.
N. multiallelic: total number of multiallelic variants.
N. SNP: total number of Single Nucleotide Polymorphism for each patient.
N. indels: total number of Insertions or Deletions for each patient.
N. transit.: number of transitions.
N. transv.: number of transversions.
Ti/TV ratio: ratio between number of transitions and transversions.
Average quality: average quality for each sample.

run	sampleID	N. variants	N. biallelic	N. multiallelic	N. SNP	N. indels	N. transit.	N. transv.	Ti/TV ratio	Average q.
1	DNA_121	395	387	8	356	72	213	110	1.936	3928.593
1	DNA_554	383	375	8	338	62	207	112	1.848	4770.656
1	DNA_571	394	384	10	347	71	204	121	1.686	4010.143
1	DNA_708	392	385	7	356	75	208	107	1.944	4255.761
1	DNA_837	461	455	6	417	74	248	139	1.784	4428.973
1	DNA_872	431	423	8	395	70	226	135	1.674	4344.959
1	DNA-223	370	364	6	339	63	202	105	1.924	5149.503
1	DNA-621	383	376	7	345	68	202	114	1.772	4750.221
1	SGT-036	409	404	5	373	70	215	123	1.748	3935.444
1	SGT-044	400	391	9	354	76	217	106	2.047	4835.095
1	SGT-047	411	404	7	374	75	216	120	1.8	3813.728
2	1091	446	442	4	415	85	248	112	2.214	4534.759
2	1138	339	331	8	310	66	175	98	1.786	4813.04
2	1179	348	342	6	319	65	183	99	1.848	5259.841
2	SGT-006	407	400	7	380	71	214	121	1.769	4586.478
2	SGT-018	382	375	7	354	64	201	116	1.733	5128.584
2	SGT-027	381	374	7	351	69	193	118	1.636	4735.668
2	SGT-031	401	395	6	368	66	218	115	1.896	4635.239
2	SGT-034	444	435	9	404	79	243	125	1.944	4628.757
2	SGT-037	385	377	8	347	62	209	113	1.85	4656.921
2	SGT-093	396	388	8	360	77	213	105	2.029	4113.088
3	1133	400	394	6	364	73	212	115	1.843	4482.541
3	1175	358	350	8	317	64	180	114	1.579	5031.737
3	SGT-002	371	361	10	336	77	190	104	1.827	5657.693
3	SGT-019	363	354	9	324	62	189	112	1.688	4785.875
3	SGT-023	364	356	8	330	63	195	105	1.857	4971.326
3	SGT-029	405	395	10	369	72	220	114	1.93	4913.511
3	SGT-030	398	387	11	366	71	213	116	1.836	4977.476
3	SGT-056	398	393	5	355	71	222	105	2.114	4011.272
3	SGT-068	405	399	6	367	83	202	120	1.683	4846.31
3	SGT-072	383	378	5	341	67	203	112	1.812	4583.872
3	SGT-081	383	376	7	344	73	202	108	1.87	4408.119
4	DNA_1101	388	384	4	367	67	223	95	2.347	14297.886
4	SGT-105	383	379	4	364	59	221	101	2.188	17177.098
4	SGT-106	359	354	5	337	53	201	107	1.879	15052.651
4	SGT-109	333	327	6	316	61	186	84	2.214	18707.734
4	SGT-111	357	354	3	338	50	200	106	1.887	16106.623
4	SGT-113	397	390	7	372	68	221	106	2.085	15822.157
4	SGT-114	413	407	6	383	68	228	113	2.018	13528.107
4	SGT-139	380	371	9	357	59	211	108	1.954	14044.355
4	SGT-142	362	360	2	333	58	192	107	1.794	10913.104
4	SGT-169	355	350	5	336	48	215	90	2.389	16838.623
4	SGT-170	428	420	8	404	68	238	116	2.052	15184.186

espinos/dnanexus_variant.txt · Last modified: 2015/07/12 15:41 by fgarcia

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