SRR8383946 170724_E00380_0422_BH3M7JCCXY_8 ATRFIB.NWD667923-1_2AMP-30 1 NIL Picard 2.6.0 2 1 FastQC 0.11.2 --disableSeqIDCheck 3 2 BWA 0.7.15 {bwa_0_7_15} mem -K 100000000 -Y -t 8 -R '{RGstring}' {reference}/reference.fa {FASTQfile1} {FASTQfile2} | {samblaster} --addMateTags -a | {samtools} view -Sbhu - | {sambamba} sort -n -t 8 --tmpdir {TMPDIR} -o {TMPDIR}/{eventId}.tmp.bam /dev/stdin 4 3 Picard 2.6.0 {java_1_8} -jar -Xmx48g {picard} MarkDuplicates I={TMPDIR}/{eventId}.tmp.bam O=/dev/stdout METRICS_FILE={TMPDIR}/mark_dups_metrics.txt ASSUME_SORT_ORDER=queryname QUIET=true COMPRESSION_LEVEL=0 | {sambamba} sort -t 8 --tmpdir {TMPDIR} -o {bamFile} /dev/stdin 5 4 samtools 1.3.1_htslib_1_3_2 Samtools flagstat 6 5 GATK 3.6 {java_1_8} -Xmx46g -jar {gatk3_6} -T BaseRecalibrator -I {bamFile} -R {reference}/reference.fa -o {recalFile} -nct 8 --downsample_to_fraction .1 -L chr1 -L chr2 -L chr3 -L chr4 -L chr5 -L chr6 -L chr7 -L chr8 -L chr9 -L chr10 -L chr11 -L chr12 -L chr13 -L chr14 -L chr15 -L chr16 -L chr17 -L chr18 -L chr19 -L chr20 -L chr21 -L chr22 -knownSites "Homo_sapiens_assembly38.dbsnp138.vcf" -knownSites "Mills_and_1000G_gold_standard.indels.hg38.vcf" -knownSites "Homo_sapiens_assembly38.known_indels.vcf" 7 6 GATK 3.6 {java_1_8} -Xmx15g -jar {gatk3_6} -T PrintReads -I {bamFile} -R {reference}/reference.fa --BQSR {recalFile} -o {recalBam} --globalQScorePrior -1.0 --useOriginalQualities --preserve_qscores_less_than 6 --static_quantized_quals 10 --static_quantized_quals 20 --static_quantized_quals 30 --disable_indel_quals 8 7 samtools 1.3.1_htslib_1_3_2 {samtools} view -C -T {reference}/reference.fa -@ 2 -o {cramFile} {recalBam} 9 8 samtools 1.3.1_htslib_1_3_2 {samtools} index -c {cramFile} {newIndex} assembly JTFH01