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Table 5 Number of SNVs called by each of the four algorithms using raw and trimmed data

From: Comparing a few SNP calling algorithms using low-coverage sequencing data

A. In raw data

 

≥ 3X*

dbSNPs

Non-dbSNPs

SOAPsnp

940

545

395

Atlas-SNP2

432

315

117

SAMtools

532

376

156

GATK-UGT

669

444

225

B. In trimmed data

 

≥ 3X*

dbSNPs

Non-dbSNPs

SOAPsnp

968

564

404

Atlas-SNP2

448

321

127

SAMtools

570

398

172

GATK-UGT

729

478

251

  1. * Atlas-SNP2 requires at least 3X to call a SNV. For the other three algorithms, we choose the called SNVs with ≥ 3X coverage.
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BMC Bioinformatics

ISSN: 1471-2105

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