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@dfjenkins3
Last active August 29, 2015 14:02
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Lumpy SV Filter Numbers, chr21 subset vs. full run

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

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
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