Table 1.

Computational steps, dependency conditions and their execution time in the NGS workflow.

Step ID	Job step name	Application name	Application module	Input file name	Application parameters	Output file name	Recommended no. of cores	Job dependency condition	% of execution time
S1	Map to Reference	BWA KIT	Seqtk, trimadap, SamTools, bwa mem, samblaster	*.fastq.gz	Default	*.bam	N/M	—	6.5%
S2	Build a standard BAM INDEX	sambamba	Index	*.bam	Default	*.bam.bai	1	S1	0.5%
S3	Realigner TargetCreator	GATK	Target creator	*.aln.bam	−T RealignerTargetCreator, −R hs37d5.fa, −known Mills_and_1000G_ gold_standard.indels.vcf.gz,	*.realigner. intervals	4 or 8	S2	3%
S4	Indel Realigner	GATK	INDEL	*aln.bam, *.realigner. intervals	−T IndelRealigner, −R hs37d5.fa, −known Mills_and_1000G _gold_standard.indels.vcf.gz, −knownIntervals	*.realigned. bam	1	S3	2%
S5	Base Recalibrator	GATK	Base Recalibration	*.realigned. bam	−T BaseRecalibrator, −R hs37d5.fa, −knownSites dbsnp_138.vcf.gz	*.recal.table	N/M	S4	13%
S6	Print Reads	GATK	Analyse the Reads	*.realigned. bam, *. recal.table	−T PrintReads, −R hs37d5.fa, −BQSR	*.realigned. recal.bam	2 or 4	S5	25%
S7	Haplotype Caller	GATK	Haplotype	*.realigned. recal.bam	−T HaplotypeCaller, −R hs37d5.fa, −pairHMM VECTOR_LOGLESS_CACHING, − −emitRef Confidence GVCF, − −variant _index_type LINEAR, − −variant_index_parameter 128000, − −dbsnp Mills_and_1000G_ gold_standard.indels.vcf.gz	*.raw.snps. indels.g.vcf	4 or 8	S6	43%
S8	Variant Recalibrator	GATK	Variant recalibration	*.realigned. bam, *.recal.table	−T BaseRecalibrator, −R hs37d5.fa, −known Mills_and_1000G_ gold_standard.indels.vcf.gz, −BQSR	*.after_recal. table	N	S5	6%
S9	Analyze Covariates	GATK	Analyse the variant	*.recal.table, *.after_ recal. table	−T AnalyzeCovariates −before −after	*.recal_plots. pdf	1	S8	1%

Where, N is the total number of cores and M is the number of CPUs.