Table 2.

Comparison to other INDEL Callers

	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

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.