Performance evaluation of pipelines for mapping, variant calling and interval padding, for the analysis of NGS germline panels

Table 2 Numbers of true positive and false positive single nucleotide variants and insertions/deletions, detected by each pipeline combination

	True positive SNVs	False positive SNVs	True positive indels	False positive indels
Null interval padding
BWA-MEM/GATK-HC	338	10	3	0
BWA-MEM/GATK-UG	342	3	0	0
BWA-MEM/SAMtools	341	3	3	0
Bowtie2/GATK-HC	295	0	3	0
Bowtie2/GATK-UG	327	39	0	0
Bowtie2/SAMtools	332	12	3	0
Stampy/GATK-HC	338	11	3	0
Stampy/GATK-UG	341	11	0	0
Stampy/SAMtools	340	2	3	0
50 bp interval padding
BWA-MEM/GATK-HC	387	12	5	9
BWA-MEM/GATK-UG	390	4	0	0
BWA-MEM/SAMtools	386	2	4	0
Bowtie2/GATK-HC	336	3	5	7
Bowtie2/GATK-UG	367	44	0	0
Bowtie2/SAMtools	376	13	4	0
Stampy/GATK-HC	387	12	5	8
Stampy/GATK-UG	389	14	0	0
Stampy/SAMtools	386	2	4	0
100 bp interval padding
BWA-MEM/GATK-HC	387	11	5	7
BWA-MEM/GATK-UG	390	5	0	0
BWA-MEM/SAMtools	387	2	4	0
Bowtie2/GATK-HC	336	3	5	7
Bowtie2/GATK-UG	369	43	0	0
Bowtie2/SAMtools	377	14	4	0
Stampy/GATK-HC	387	11	5	9
Stampy/GATK-UG	388	13	0	0
Stampy/SAMtools	386	3	4	0
BWA enrichment	341	3	3	0

For pipeline performance evaluation, variants were categorized in four groups; exonic single nucleotide variants (SNVs) and exonic indels (insertions or deletions), intronic SNVs (± 1 to ± 10) and intronic indels (± 1– ± 10). Sanger sequencing was performed to validate the calls. GATK Genome Analysis ToolKit, HC HaplotypeCaller; indels, insertions & deletions, SNVs single nucleotide variants, UG UnifiedGenotyper

ISSN: 1471-2105