转换成BAM文件，sort, mark duplicates

java -jar $picard SortSam \    INPUT=aligned_sample1.sam \    OUTPUT=sorted_sample1.bam \    SORT_ORDER=coordinate java -jar $picard MarkDuplicates \    INPUT=sorted_sample1.bam \    OUTPUT=dedup_sample1.bam \    METRICS_FILE=metrics_sample1.txt #just mark, not remove. most tools in GATK will ingore the marked reads；If desired, duplicates can be removed using the REMOVE_DUPLICATE and REMOVE_SEQUENCING_DUPLICATES options. java -jar $picard BuildBamIndex \