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Table 2 Comparison to other INDEL Callers

From: An integrative variant analysis suite for whole exome next-generation sequencing data

  Atlas-Indel2 GATK Unified Genotyper SAMtools mpileup
Average INDELs/sample
(Coding and Non-coding)
23525 9648 26139
Average Coding INDELs/sample 194 1947 1560
Average % 3(n) Coding INDELs/sample 47.52 10.39 25.82
# Coding INDELs 816 12027 12305
% 3(n) Coding INDELs 38.11 7.78 23.84
# Non-coding INDELs 19607 3441 28135
% 3(n) Non-coding INDELs 14.06 9.79 17.19
  1. Summary of INDELs called by Atlas-Indel2, GATK Unified Genotyper and SAMtools mPileup on 10 SOLiD samples (5 LWK, 5 CEU). The metrics compared are the average number of coding and non-coding INDELs per sample, the number of INDEL alleles merged across all 10 samples and the % 3(n) INDELs. The 3(n) INDELs refer to INDELs with a length of multiples of 3, which do not cause a frameshift mutation in the coding region. Previous studies have reported that coding regions tend to harbor less frameshift-causing INDELs. Coding refers to the consensus exome target regions of the genome as defined by the 1000 Genomes consortium. Non-coding refers to all the regions outside of the exome target regions. In the merged call sets, INDELs at the same site found in different samples are merged together in a population VCF file. Individual sample results are shown in Additional file 2.