Table 3.

The sequencing samples analysed in benchmarking.

Sample	Dataset	Coverage
TCGA-A6-2681-10A-01D-2188-10 (COAD)	TCGA: Colon adenocarcinoma	50×
TCGA-HC-7233-10A-01D-2115-08 (PRAD)	TCGA: Prostate adenocarcinoma	50×
TCGA-NJ-A4YQ-10A-01D-A46J-10 (LUAD)	TCGA: Lung adenocarcinoma	50×
TCGA-BW-A5NQ-10A-01D-A27I-10 (LIHC)	TCGA: Liver hepatocellular carcinoma	45×
NA12878	1K Genomes: CEU pedigree (Offspring)	50×
NA12891	1K Genomes: CEU pedigree (Father)	50×
NA12892	1K Genomes: CEU pedigree (Mother)	50×
HK2_Enrich01	NA	500×
HK2_Enrich02	NA	500×

All TCGA samples were DNA derived from peripheral blood and were sequenced with Illumina platform for whole genome sequencing. CEU pedigree samples derived from immortalised cell lines maintained by 1000 Genomes Project and were sequenced with Illumina platform for whole genome sequencing. Target enrichment samples were germline derived and sequenced as described in the methods section.