SRR5338640 160613_ST-E00270_0222_BHNVK7CCXX_6_1 GMKFEE.CDD-CFI-001-1_3AMP-22 1 NIL Picard 1.128 2 1 FastQC 0.11.2 --disableSeqIDCheck 3 2 BWA 0.7.12 BWA mem -M -t 8 -R | samtools view -F 256 -Sbh 4 3 BWA 0.7.12 BWA mem -M -t 8 -R | samtools fixmate 5 4 sambamba 0.5.9 sambamba markdup -t 8 -p 6 5 sambamba 0.5.9 sambamba index -t 8 7 6 verifyBamID 1.1.0 verifyBamID --vcf HapMapMAF.vcf --verbose --ignoreRG 8 7 GATK 3.4.0 {java} -Xmx46g -jar {gatk} -T RealignerTargetCreator -I {bamFile} -R {reference} -nt 8 --downsampling_type NONE -known {ThousandGenomeInDels} -known {MillsInDels} -o {realignIntervals} 9 8 GATK 3.4.0 {java} -Xmx46g -jar {gatk} -T IndelRealigner -R {reference} -I {bamFile} -targetIntervals {realignIntervals} --downsampling_type NONE --consensusDeterminationModel USE_READS -known {ThousandGenomeInDels} -known {MillsInDels} -o {realignBam} 10 9 GATK 3.4.0 {java} -Xmx46g -jar {gatk} -T BaseRecalibrator -I {realignBam} -R {reference} -o {recalFile} -nct 8 --downsampling_type NONE -knownSites {dbSNP} -knownSites {ThousandGenomeInDels} -knownSites {MillsInDels} -cov ReadGroupCovariate -cov QualityScoreCovariate -cov CycleCovariate -cov ContextCovariate 11 10 GATK 3.4.0 {java} -Xmx46g -Djava.io.tmpdir={TMPDIR} -jar {gatk} -T PrintReads -I {realignBam} -R {reference} -BQSR {recalFile} --emit_original_quals --downsampling_type NONE -nct 4 -o {recalBam} 12 11 ATLAS v0.0.1-rc7 {atlas} --bam {bamFile} --samplename {sampleName} --prefix {varOut} --ref {reference} --runGL true 13 12 Cassandra 15.4.29 {java} -jar -Xms47g -Xmx47g {CassandraJAR} --tempDir {TMPDIR} -t Annotate -n 8 -a 1 -i {vcfFile} -p {pileupFile} --annovarPath {Annovar} --annovarDB {AnnovarDB} --annotationSources {AnnotationSources} 14 13 bamUtil 1.0.13 {bamUtil} squeeze --in {bamFile} --out {tmpBam} --keepDups --binMid --rmTags "BI:Z;BD:Z;PG:Z" --binQualS 2,3,10,20,25,30,35,40,50 assembly GRCh37.p4