Lumpy SV Filter Numbers, chr21 subset vs. full run

filter_counts.md

Chromosome 21 Subset, no filter applied

Run	chr21 subset	chr21 subset	chr21 subset
Exclude	none	lcr	speedseq
Filter	all	all	all
Deletions	212	186	116
Duplications	43	36	11
Interchroms	5	5	0
Inversions	10	9	7

Full CEU run, no filter applied

Run	full CEU	full CEU	full CEU
Exclude	none	lcr	speedseq
Filter	all	all	all
Deletions	201	177	98
Duplications	55	45	13
Interchroms	518	435	47
Inversions	14	13	7

Chromosome 21 Subset, pass filter

Run	chr21 subset	chr21 subset	chr21 subset
Exclude	none	lcr	speedseq
Filter	PASS	PASS	PASS
Deletions	85	72	30
Duplications	31	28	8
Interchroms	1	1	0
Inversions	5	5	2

Full CEU run, pass filter

Run	full CEU	full CEU	full CEU
Exclude	none	lcr	speedseq
Filter	PASS	PASS	PASS
Deletions	92	82	27
Duplications	36	31	9
Interchroms	245	210	16
Inversions	6	5	3

sensitivity.md

Chromosome 21 Subset, no filter applied

Run	chr21 subset	chr21 subset	chr21 subset
Exclude	none	lcr	speedseq
Filter	all	all	all
Concordant	39	27	34
Discordant FN	39	52	44
Discordant FP	173	159	82
Sensitivity	0.50	0.34	0.44
Precision	0.18	0.15	0.29

Full CEU run, no filter applied

Run	full CEU	full CEU	full CEU
Exclude	none	lcr	speedseq
Filter	all	all	all
Concordant	35	25	30
Discordant FN	43	54	48
Discordant FP	166	152	68
Sensitivity	0.45	0.32	0.38
Precision	0.17	0.14	0.31

Chromosome 21 Subset, pass filter

Run	chr21 subset	chr21 subset	chr21 subset
Exclude	none	lcr	speedseq
Filter	PASS	PASS	PASS
Concordant	25	18	21
Discordant FN	53	61	57
Discordant FP	60	54	9
Sensitivity	0.32	0.23	0.27
Precision	0.29	0.25	0.70

Full CEU run, pass filter

Run	full CEU	full CEU	full CEU
Exclude	none	lcr	speedseq
Filter	PASS	PASS	PASS
Concordant	23	18	20
Discordant FN	55	61	58
Discordant FP	69	64	7
Sensitivity	0.29	0.23	0.26
Precision	0.25	0.22	0.74