MiSeq Reporter Inbuilt Pipeline

8/14/2013,21:57:39.431,Launch: C:\Illumina\MiSeq Reporter\bwa.exe aln -t 8 -q 15 -f "\\Server\NGSData\DATA\130813_M00794_0097_000000000-A5CCC\Data\Intensities\BaseCalls\Alignment\2013-203-025-NGSPCD_S1_L001_R1_001.sai" "C:\Illumina\MiSeq Reporter\Genomes\Homo_sapiens\UCSC\hg19\Sequence\WholeGenomeFASTA\genome.fa" "\\Server\NGSData\DATA\130813_M00794_0097_000000000-A5CCC\Data\Intensities\BaseCalls\2013-203-025-NGSPCD_S1_L001_R1_001.fastq.gz"

8/14/2013,22:43:34.793,Launch: C:\Illumina\MiSeq Reporter\bwa.exe aln -t 8 -q 15 -f "\\Server\NGSData\DATA\130813_M00794_0097_000000000-A5CCC\Data\Intensities\BaseCalls\Alignment\2013-203-025-NGSPCD_S1_L001_R2_001.sai" "C:\Illumina\MiSeq Reporter\Genomes\Homo_sapiens\UCSC\hg19\Sequence\WholeGenomeFASTA\genome.fa" "\\Server\NGSData\DATA\130813_M00794_0097_000000000-A5CCC\Data\Intensities\BaseCalls\2013-203-025-NGSPCD_S1_L001_R2_001.fastq.gz"

8/14/2013,23:37:15.685,Launch: C:\Illumina\MiSeq Reporter\bwa.exe sampe -b -t 8 -r "@RG\tID:2013-203-025\tSM:2013-203-025" -f "\\Server\NGSData\DATA\130813_M00794_0097_000000000-A5CCC\Data\Intensities\BaseCalls\Alignment\2013-203-025-NGSPCD_S1_L001_R1_001.uncompressed.bam" -T 17 "C:\Illumina\MiSeq Reporter\Genomes\Homo_sapiens\UCSC\hg19\Sequence\WholeGenomeFASTA\genome.fa" "\\Server\NGSData\DATA\130813_M00794_0097_000000000-A5CCC\Data\Intensities\BaseCalls\Alignment\2013-203-025-NGSPCD_S1_L001_R1_001.sai" "\\Server\NGSData\DATA\130813_M00794_0097_000000000-A5CCC\Data\Intensities\BaseCalls\Alignment\2013-203-025-NGSPCD_S1_L001_R2_001.sai" "\\Server\NGSData\DATA\130813_M00794_0097_000000000-A5CCC\Data\Intensities\BaseCalls\2013-203-025-NGSPCD_S1_L001_R1_001.fastq.gz" "\\Server\NGSData\DATA\130813_M00794_0097_000000000-A5CCC\Data\Intensities\BaseCalls\2013-203-025-NGSPCD_S1_L001_R2_001.fastq.gz"

8/15/2013,01:01:32.062,Launch: C:\Illumina\MiSeq Reporter\samtools.exe sort "\\Server\NGSData\DATA\130813_M00794_0097_000000000-A5CCC\Data\Intensities\BaseCalls\Alignment\2013-203-025-NGSPCD_S1_L001_R1_001.uncompressed.bam" "\\Server\NGSData\DATA\130813_M00794_0097_000000000-A5CCC\Data\Intensities\BaseCalls\Alignment\2013-203-025-NGSPCD_S1.merged"

8/15/2013,01:45:37.125,Launch: C:\Illumina\MiSeq Reporter\samtools.exe rmdup -m "\\Server\NGSData\DATA\130813_M00794_0097_000000000-A5CCC\Data\Intensities\BaseCalls\Alignment\2013-203-025-NGSPCD_S1.merged.bam" "\\Server\NGSData\DATA\130813_M00794_0097_000000000-A5CCC\Data\Intensities\BaseCalls\Alignment\2013-203-025-NGSPCD_S1.bam"

8/15/2013,02:10:03.697,Launch: C:\Illumina\MiSeq Reporter\samtools.exe index "\\Server\NGSData\DATA\130813_M00794_0097_000000000-A5CCC\Data\Intensities\BaseCalls\Alignment\2013-203-025-NGSPCD_S1.bam"

8/15/2013,02:12:37.683,>>>Total BAM indexing time: 00:02:34.0
8/15/2013,02:12:37.698,Elapsed time (step/time(sec)/name)    3    15298.3    Alignment

8/15/2013,02:12:37.714,Step 4 : Variant analysis
8/15/2013,02:12:37.730,Launch: C:\Illumina\MiSeq Reporter\jre-6u31\bin\java.exe -Xmx8g -jar "C:\Illumina\MiSeq Reporter\GenomeAnalysisTK.jar" -T UnifiedGenotyper -l INFO -glm BOTH -et NO_ET -stand_call_conf 30 -stand_emit_conf 10 -R "C:\Illumina\MiSeq Reporter\Genomes\Homo_sapiens\UCSC\hg19\Sequence\WholeGenomeFASTA\genome.fa" -nt 8 -I "\\Server\NGSData\DATA\130813_M00794_0097_000000000-A5CCC\Data\Intensities\BaseCalls\Alignment\2013-203-025-NGSPCD_S1.bam" -o "\\Server\NGSData\DATA\130813_M00794_0097_000000000-A5CCC\Data\Intensities\BaseCalls\Alignment\variants_G1.1.vcf"