Analysis notebooks (#356)

Update to analysis notebooks
kevlar-dev · Feb 8, 2019 · 0cfd001 · 0cfd001
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commit 0cfd001
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Showing 64 changed files with 13,790 additions and 767 deletions.
diff --git a/notebook/bigsim/JointCall-10x-PBT.mvf b/notebook/bigsim/JointCall-10x-PBT.mvf
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+CHROM	POS	AC	FAMILY	TP	MOTHER_GT	MOTHER_DP	MOTHER_AD	MOTHER_PL	FATHER_GT	FATHER_DP	FATHER_AD	FATHER_PL	CHILD_GT	CHILD_DP	CHILD_AD	CHILD_PL
+chr17	105266	1	10	5	C|C	2	2,0	0,6,52	./.	-1	.	.	C|A	4	2,2	41,0,39
+chr17	753396	4	10	11	G|G	7	0,7	194,21,0	./.	-1	.	.	G|G	4	0,4	111,12,0
+chr17	2920041	1	10	16	G|G	6	6,0	0,18,166	./.	-1	.	.	G|T	15	7,8	177,0,149
+chr17	4784742	2	10	null	./.	-1	.	.	CAAAA/C	7	2,5	204,0,69	CAAAA/C	3	2,1	36,0,81
+chr17	5498642	2	10	null	./.	-1	.	.	T/A	5	4,1	13,0,96	T/A	11	7,4	78,0,161
+chr17	11071638	2	10	63	C/T	7	3,4	90,0,62	./.	-1	.	.	C/T	9	5,4	84,0,112
+chr17	12443823	4	10	null	./.	-1	.	.	A|A	14	0,14	544,42,0	A|A	5	0,5	208,15,0
+chr17	13668435	2	10	null	./.	-1	.	.	C/T	8	4,4	87,0,87	C/T	11	4,7	161,0,78
+chr17	19188242	2	10	null	./.	-1	.	.	A|A	2	0,2	55,6,0	T|A	1	1,0	0,3,28
+chr17	20549234	3	10	5	G|G	2	0,2	55,6,0	./.	-1	.	.	G|C	4	3,1	16,0,71
+chr17	22379428	1	10	5	G|G	2	2,0	0,6,55	./.	-1	.	.	G|T	3	1,2	46,0,19
+chr17	22761025	1	10	10	A|A	4	4,0	0,12,107	./.	-1	.	.	A|G	5	1,4	90,0,12
+chr17	24154512	2	10	null	./.	-1	.	.	C|C	2	0,2	52,6,0	A|C	1	1,0	0,3,28
+chr17	24420608	1	10	null	./.	-1	.	.	C|C	1	1,0	0,3,28	A|C	5	3,2	40,0,68
+chr17	24866367	1	10	null	./.	-1	.	.	A|A	1	1,0	0,3,28	C|A	5	3,2	38,0,63
+chr17	24866398	1	10	null	./.	-1	.	.	T|T	1	1,0	0,3,28	A|T	5	3,2	37,0,64
+chr17	25324640	1	10	null	./.	-1	.	.	A|A	1	1,0	0,3,28	C|A	4	2,2	43,0,43
+chr17	26305372	1	10	null	./.	-1	.	.	T|T	4	4,0	0,12,111	G|T	4	2,2	43,0,43
+chr17	35998212	1	10	null	./.	-1	.	.	G|G	11	11,0	0,33,305	C|G	12	5,7	158,0,103
+chr17	36429017	3	10	null	./.	-1	.	.	C|C	3	0,3	83,9,0	T|C	7	3,4	90,0,62
+chr17	36523196	2	10	null	./.	-1	.	.	A|A	4	4,0	0,12,111	C|A	9	5,4	84,0,111
+chr17	37750996	4	10	19	C|C	7	0,7	194,21,0	./.	-1	.	.	C|C	8	0,8	222,24,0
+chr17	38431140	2	10	24	C|C	9	9,0	0,27,250	./.	-1	.	.	C|G	7	5,2	34,0,118
+chr17	38776218	2	10	null	./.	-1	.	.	C/T	8	4,4	87,0,87	C/T	16	7,9	202,0,146
+chr17	40941321	2	10	57	G/A	11	6,5	106,0,133	./.	-1	.	.	G/A	9	3,6	139,0,56
+chr17	43975995	4	10	null	./.	-1	.	.	C|C	8	0,8	222,24,0	C|C	5	0,5	139,15,0
+chr17	44640386	3	10	null	./.	-1	.	.	G|G	15	0,15	416,45,0	A|G	11	3,8	189,0,50
+chr17	44961591	2	10	null	./.	-1	.	.	C|C	10	10,0	0,30,263	CA|C	7	2,5	110,0,31
+chr17	46242799	1	10	null	./.	-1	.	.	C|C	2	2,0	0,6,55	T|C	3	1,2	46,0,19
+chr17	46475979	1	10	null	./.	-1	.	.	T|T	1	1,0	0,3,26	G|T	3	1,2	46,0,19
+chr17	46657812	2	10	3	T|A	1	1,0	0,3,28	./.	-1	.	.	T|T	2	0,2	55,6,0
+chr17	59634763	2	10	35	G|G	15	15,0	0,45,416	./.	-1	.	.	G|A	12	1,11	277,8,0
+chr17	65681675	2	10	null	./.	-1	.	.	A|A	7	7,0	0,21,170	AT|A	9	4,5	89,0,71
+chr17	69557676	1	10	3	CTACGATTCTGAGTTAATTGTTTGTTTCTGTGTTTTTTTTTTTTTTTTTTTCGAGATGGAGTCTTGCTCTGTCGCCCAGCCTGGAGTGCAATGGTGCGATCTCGGCTCACTGCAACCTCCACCTCCCAGGTTCAAGTGATCCTCCTGCCTCAGCCTCACAAGTAGCAGGGATTAAAGACATGTG/CTACGATTCTGAGTTAATTGTTTGTTTCTGTGTTTTTTTTTTTTTTTTTTTCGAGATGGAGTCTTGCTCTGTCGCCCAGCCTGGAGTGCAATGGTGCGATCTCGGCTCACTGCAACCTCCACCTCCCAGGTTCAAGTGATCCTCCTGCCTCAGCCTCACAAGTAGCAGGGATTAAAGACATGTG	22	22,0	0,66,1052	CTACGATTCTGAGTTAATTGTTTGTTTCTGTGTTTTTTTTTTTTTTTTTTTCGAGATGGAGTCTTGCTCTGTCGCCCAGCCTGGAGTGCAATGGTGCGATCTCGGCTCACTGCAACCTCCACCTCCCAGGTTCAAGTGATCCTCCTGCCTCAGCCTCACAAGTAGCAGGGATTAAAGACATGTG/CTACGATTCTGAGTTAATTGTTTGTTTCTGTGTTTTTTTTTTTTTTTTTTTCGAGATGGAGTCTTGCTCTGTCGCCCAGCCTGGAGTGCAATGGTGCGATCTCGGCTCACTGCAACCTCCACCTCCCAGGTTCAAGTGATCCTCCTGCCTCAGCCTCACAAGTAGCAGGGATTAAAGACATGTG	21	21,0	0,63,945	CTACGATTCTGAGTTAATTGTTTGTTTCTGTGTTTTTTTTTTTTTTTTTTTCGAGATGGAGTCTTGCTCTGTCGCCCAGCCTGGAGTGCAATGGTGCGATCTCGGCTCACTGCAACCTCCACCTCCCAGGTTCAAGTGATCCTCCTGCCTCAGCCTCACAAGTAGCAGGGATTAAAGACATGTG/C	16	10,6	104,0,427
+chr17	77821378	1	10	4	ACGGTCCCTGCAGGTGGCCAGCCCAGGGGGAGAGACCAAGAGTGGGCTGTGGCTTTCACTTTTGGCCATGGTCAAAGACTTCACCTCGGCCGGTCTCCAGCAGATGTCCTCTCCTGGTCATAACAGTCAGGGCAGCTGGGCATGGT/ACGGTCCCTGCAGGTGGCCAGCCCAGGGGGAGAGACCAAGAGTGGGCTGTGGCTTTCACTTTTGGCCATGGTCAAAGACTTCACCTCGGCCGGTCTCCAGCAGATGTCCTCTCCTGGTCATAACAGTCAGGGCAGCTGGGCATGGT	21	21,0	0,63,945	ACGGTCCCTGCAGGTGGCCAGCCCAGGGGGAGAGACCAAGAGTGGGCTGTGGCTTTCACTTTTGGCCATGGTCAAAGACTTCACCTCGGCCGGTCTCCAGCAGATGTCCTCTCCTGGTCATAACAGTCAGGGCAGCTGGGCATGGT/ACGGTCCCTGCAGGTGGCCAGCCCAGGGGGAGAGACCAAGAGTGGGCTGTGGCTTTCACTTTTGGCCATGGTCAAAGACTTCACCTCGGCCGGTCTCCAGCAGATGTCCTCTCCTGGTCATAACAGTCAGGGCAGCTGGGCATGGT	25	25,0	0,74,1122	ACGGTCCCTGCAGGTGGCCAGCCCAGGGGGAGAGACCAAGAGTGGGCTGTGGCTTTCACTTTTGGCCATGGTCAAAGACTTCACCTCGGCCGGTCTCCAGCAGATGTCCTCTCCTGGTCATAACAGTCAGGGCAGCTGGGCATGGT/A	12	7,5	189,0,259
+chr17	81038907	2	10	null	./.	-1	.	.	G|G	10	10,0	0,30,312	A|G	9	5,4	84,0,112
diff --git a/notebook/bigsim/JointCall-10x-TDN.vcf b/notebook/bigsim/JointCall-10x-TDN.vcf
diff --git a/notebook/bigsim/JointCall-20x-PBT.mvf b/notebook/bigsim/JointCall-20x-PBT.mvf
diff --git a/notebook/bigsim/JointCall-20x-TDN.vcf b/notebook/bigsim/JointCall-20x-TDN.vcf
diff --git a/notebook/bigsim/JointCall-30x-PBT.mvf b/notebook/bigsim/JointCall-30x-PBT.mvf
diff --git a/notebook/bigsim/JointCall-30x-TDN.vcf b/notebook/bigsim/JointCall-30x-TDN.vcf
diff --git a/notebook/bigsim/JointCall-50x-PBT.mvf b/notebook/bigsim/JointCall-50x-PBT.mvf
diff --git a/notebook/bigsim/JointCall-50x-TDN.vcf b/notebook/bigsim/JointCall-50x-TDN.vcf