Table 1.
Computational approach to genome analysis using the massively parallel Cray XE6 supercomputer
| Step | Program | Module/Call | Input | Parameters | Output | Number per genome | Number of active cores/node | Number nodes | Concurrency |
|---|---|---|---|---|---|---|---|---|---|
| Extract fastq | Picard 1.98 | SamToFastq | bam | default | fastq | 2(#RGs) | 1 | 1 | 1 |
| Alignment | BWA 0.5.9 | bwa aln | fastq | -qtrim 15 | sai file | 2(#RGs) | 24 | 2(#RGs) | 24(#RGs) |
| Convert sai to sam | BWA tpx 0.5.9 | bwa sampe | sai | -T –X –P (BWA) | sam | 2(#RGs) | ∼24 | #RGs | 24(#RGs) |
| Compression | samtools 0.1.18 | view | sam | -bo (samtools) | bam | 2(#RGs) | 3 | #RGs | 1(#RGs) |
| Split | samtools 0.1.18 | view/merge | bam | -h (preserve readgroup) | bam | 25 | 24 | 1 | 25 |
| Sort | Picard 1.98 | SortSam | bam | -coordinate | bam | 25 | 4 + GC | ∼6 | 25 |
| Mark duplicates | Picard 1.98 | Mark | bam | -REMOVE_DUPLICATES | bam | 25 | 4 + GC | ∼6 | 25 (each with 3 threads) |
| Duplicates | false | ||||||||
| Reorder | Picard 1.98 | ReorderSam | bam | default | bam | 25 | 4 + GC | ∼6 | 25 (GCa) |
| Identify indel realignment targets | GATK 2.7-1 | GATK | bam | -T RealignerTargetCreator | intervals | 25 | 4 + GC | ∼6 | 25 (GC) |
| -L <chromosome ID> | |||||||||
| Realign targeted intervals | GATK 2.7-1 | GATK | bam | -T IndelRealigner | bam | 25 | 4 + GC | ∼6 | 25 (GC) |
| -targetIntervals <intervals> | |||||||||
| -LOD 5 | |||||||||
| -L <chromosome ID> | |||||||||
| Base recalibrator | GATK 2.7-1 | GATK | bam | -T BaseRecalibrator | csv | 25 | 4 + GC | ∼6 | 25 (GC) |
| -cov ReadGroupCovariate | |||||||||
| -cov QualityScoreCovariate | |||||||||
| -cov CycleCovariate | |||||||||
| -cov ContextCovariate | |||||||||
| -knownSites dbSNP_135 | |||||||||
| Print reads | GATK 2.7-1 | GATK | bam | -T PrintReads | bam | 25 | 4 + GC | ∼6 | 25 (GC) |
| -baq RECALCULATE | |||||||||
| -baqGOP 30 | |||||||||
| -BQSR <csv file> | |||||||||
| Call variants | GATK 2.7-1 | GATK | bam | -T Haplotype Caller | vcf | 25 | |||
| -L <chromosome ID> | |||||||||
| -D dbSNP_135.hg19.vcf | |||||||||
| -A AlleleBalance | |||||||||
| -A Coverage | |||||||||
| -A HomopolymerRun | |||||||||
| -A FisherStrand | |||||||||
| -A HaplotypeScore | |||||||||
| -A HardyWeinberg | |||||||||
| -A ReadPosRankSumTest | |||||||||
| -A QualByDepth | |||||||||
| -A MappingQualityRankSumTest | |||||||||
| -A VariantType | |||||||||
| -A MappingQualityZero | |||||||||
| -minPruning 10 | |||||||||
| -stand_call_conv 30.0 | |||||||||
| -stand_emit_conv 10.0 | |||||||||
| Filter variants | GATK 2.7-1 | GATK | bam | -T VariantFiltration | vcf | 25 | 4 + GC | ∼6 | 25 (GC) |
| -L <chromosome ID> | |||||||||
| –clusterWindowSize 10 | |||||||||
| –filterExpression “(AB?: 0) > 0.75 || -QUAL < 30.0 || DP > 360 || SB > −0.1 || MQ0 ≥ 10” | |||||||||
| Annotate variants | snpEff 2.0.5 | snpEff | vcf | default | vcf | 25 | 4 | ∼6 |
Note: RG = readgroup. aGC = 2 threads used for java Garbage Collection.