Skip to main content
Fig. 2 | Genome Medicine

Fig. 2

From: ScanIndel: a hybrid framework for indel detection via gapped alignment, split reads and de novo assembly

Fig. 2

Effect of different strategies on indel detection. ScanIndel is executed by three modes: (1) BWA-MEM alignment + soft-clipping realignment + FreeBayes indel calling (labeled as ‘scanindel_mapping_only’); (2) BWA-MEM alignment + de novo assembly + FreeBayes indel calling (labeled as ‘scanindel_assembly_only’); and (3) complete ScanIndel procedures — BWA-MEM alignment + softclipping realignment + de novo assembly + FreeBayes indel calling (labeled as ‘scanindel’). In addition, FreeBayes indel calling directly from BWA-MEM alignment is tested as well (labeled as ‘freebayes’). Smoothed histograms (40-bp bins) showed the comparison on simulated short reads 100 bp and 200 bp in length under 10×, 20× and 50× mean coverage for detecting 1000 deletions and 1000 insertions ranged evenly in size from 1 bp to 1 kb

Back to article page

Genome Medicine

ISSN: 1756-994X

Contact us