I have a sample's data, using illumina 's Piar End sequencing technology.
RE19E2T40PA_L1_I040.pairPrimer_1.fastq (Read1)
RE19E2T40PA_L1_I040.pairPrimer_2.fastq (Read2)
I have aligned both Read1 and Read2 to hg19 using BWA, and generated three bam file.RE19E2T40PA_L1_I040.pairPrimer_1.fastq.read1.sorted.bam (Read1's bam file, generated via command :' bwa samse' )
RE19E2T40PA_L1_I040.pairPrimer_1.fastq.read2.sorted.bam (Read2's bam file, generated via command :' bwa samse' )
RE19E2T40PA_L1_I040.pairPrimer_1.fastq.sorted.bam (pair end bam file, generated via command :' bwa sampe' )
Then I using picard to generate alignment statistics.
java -jar /usr/app/picard/picard-tools-1.77/CollectAlignmentSummaryMetrics.jar R=/home/share/hg19/ucsc.hg19.fasta I=RE19E2T40PA_L1_I040.pairPrimer_1.fastq.read1.sorted.bam O=RE19E2T40PA_L1_I040.pairPrimer_1.fastq.read1.sorted.bam.stat
java -jar /usr/app/picard/picard-tools-1.77/CollectAlignmentSummaryMetrics.jar R=/home/share/hg19/ucsc.hg19.fasta I=RE19E2T40PA_L1_I040.pairPrimer_1.fastq.read2.sorted.bam O=RE19E2T40PA_L1_I040.pairPrimer_1.fastq.read2.sorted.bam.stat
java -jar /usr/app/picard/picard-tools-1.77/CollectAlignmentSummaryMetrics.jar R=/home/share/hg19/ucsc.hg19.fasta I=RE19E2T40PA_L1_I040.pairPrimer_1.fastq.sorted.bam O=RE19E2T40PA_L1_I040.pairPrimer_1.fastq.sorted.bam.stat