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Table 3 Comparing the performance of HAPDeNovo using HP1 and HP2 only versus HP0, HP1 and HP2 (both with TrioDeNovo as input), with DQ = 7 and sequencing depth changing from 10 to 20

From: HAPDeNovo: a haplotype-based approach for filtering and phasing de novo mutations in linked read sequencing data

 

Depth

10

11

12

13

14

15

16

17

18

19

20

TrioDeNovo

TP

44

44

44

44

44

44

43

42

41

39

36

FP

3932

3926

3923

3862

3789

3673

3532

3410

3250

3106

2969

HAPDeNovo

TP

40

40

40

40

40

40

40

39

39

37

35

by HP1, HP2

FP

605

604

603

584

557

521

481

453

423

394

372

HAPDeNovo

TP

44

44

44

44

44

44

43

42

41

39

36

by HP1, HP2, HP0

FP

768

766

765

744

715

674

626

593

558

525

496

  1. TP (True Positive): Number of DNMs in candidate plus gold standard. FP (False Positive): Number of DNMs in the candidate set but not in the gold standard
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BMC Genomics

ISSN: 1471-2164

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