SRR1729000 0533_20100708_1_SP_AZZ_MID0048_ZZ_sA_01003311432_4_BC2 TEST.A04848-2_1PRE-9 1 NIL bfast 0.6.3c solid2fastq -n 10000000 -o [run name] [input csfasta] [input qual] 2 1 bfast 0.6.3c bfast match -A 1 -t -n 8 -f [path to reference] -T [temp directory] -r [path to fastq file] 3 2 bfast 0.6.3c bfast localalign -A 1 -t -n 8 -f [path to reference] -m [path to bfast matches file (bmf)] 4 3 bfast 0.6.3c bfast postprocess -f [path to reference] -i [path to baf file] -a 3 -O 1 5 4 picard tools 1.07 java -jar -Xmx4g SamFormatConverter.jar TMP_DIR=[temp directory] INPUT=[input sam path] OUTPUT=[output bam path] VALIDATION_STRINGENCY=STRICT 6 5 picard tools 1.07 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 1.07 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 1.07 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 1.07 java -Xmx6000M CaptureStatsBAM5 -o [output directory] -t [chip design] -i [input bam] -w -d SRR1729001 0533_20100708_1_SP_AZZ_ZZ_BoerBCPool_10_17sA_01003311432_2_BC2 TEST.A04848-2_1PRE-9 1 NIL bfast 0.6.3c solid2fastq -n 10000000 -o [run name] [input csfasta] [input qual] 2 1 bfast 0.6.3c bfast match -A 1 -t -n 8 -f [path to reference] -T [temp directory] -r [path to fastq file] 3 2 bfast 0.6.3c bfast localalign -A 1 -t -n 8 -f [path to reference] -m [path to bfast matches file (bmf)] 4 3 bfast 0.6.3c bfast postprocess -f [path to reference] -i [path to baf file] -a 3 -O 1 5 4 picard tools 1.07 java -jar -Xmx4g SamFormatConverter.jar TMP_DIR=[temp directory] INPUT=[input sam path] OUTPUT=[output bam path] VALIDATION_STRINGENCY=STRICT 6 5 picard tools 1.07 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 1.07 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 1.07 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 1.07 java -Xmx6000M CaptureStatsBAM5 -o [output directory] -t [chip design] -i [input bam] -w -d SRR1729002 0100_20100716_1_SP_AZZ_ZZ_BoerBCPool_10_15sA_01003311484_1_BC2 TEST.A04848-2_1PRE-9 1 NIL bfast 0.6.3c solid2fastq -n 10000000 -o [run name] [input csfasta] [input qual] 2 1 bfast 0.6.3c bfast match -A 1 -t -n 8 -f [path to reference] -T [temp directory] -r [path to fastq file] 3 2 bfast 0.6.3c bfast localalign -A 1 -t -n 8 -f [path to reference] -m [path to bfast matches file (bmf)] 4 3 bfast 0.6.3c bfast postprocess -f [path to reference] -i [path to baf file] -a 3 -O 1 5 4 picard tools 1.07 java -jar -Xmx4g SamFormatConverter.jar TMP_DIR=[temp directory] INPUT=[input sam path] OUTPUT=[output bam path] VALIDATION_STRINGENCY=STRICT 6 5 picard tools 1.07 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 1.07 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 1.07 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 1.07 java -Xmx6000M CaptureStatsBAM5 -o [output directory] -t [chip design] -i [input bam] -w -d