SRR564078 SRR351060 110124_SN166_0163_A15006043_3 SRX100024 ING_AMLSRG.PANLRE03-1_1pA_1 1 NIL bfast 0.6.4d solid2fastq –n 10000000 –o [run name] [input csfasta] [input qual] 2 1 bfast 0.6.4d bfast match -A 1 -t -n 8 –f [path to reference] -T [temp directory] -r [path to fastq file] 3 2 bfast 0.6.4d bfast localalign -A 1 -t -n 8 –f [path to reference] -m [path to bfast matches file (bmf)] 4 3 bfast 0.6.4d bfast postprocess –f [path to reference] -i [path to baf file] -a 3 -O 1 5 4 picard tools 1.41 java -jar -Xmx4g SamFormatConverter.jar TMP_DIR=[temp directory] INPUT=[input sam path] OUTPUT=[output bam path] VALIDATION_STRINGENCY=STRICT 6 5 picard tools 1.41 java -jar -Xmx4g MergeSamFiles.jar TMP_DIR=[temp directory] INPUT=[input split bam path] OUTPUT=[output merge bam path] VALIDATION_STRINGENCY=STRICT 6 5 picard tools 1.41 java -jar -Xmx4g SortSam.jar TMP_DIR=[temp directory] INPUT=[input merge bam path] OUTPUT=[output sorted bam path] SORT_ORDER=coordinate VALIDATION_STRINGENCY=STRICT 7 6 picard tools 1.41 java -jar -Xmx4g MarkDuplicates.jar TMP_DIR=[temp directory] INPUT=[input sorted bam path] OUTPUT=[output marked dupes bam path] METRICS_FILE='./metric_file.picard' VERBOSITY=ERROR VALIDATION_STRINGENCY=STRICT 8 7 raw bam read validator 1.0 java -jar /raw.bam.reads.validator.jar [bam] [input directory] [output log] 9 8 picard tools 1.41 java -Xmx6000M CaptureStatsBAM5 -o [output directory] -t [chip design] -i [input bam] -w -d assembly GRCh37-lite