最后:samtools markdup -r xxx.sortposition.bam xxx.markdup.bam #加上-r就会直接去掉重复序列 (6) 用picard MarkDuplicates去重复 # picard MarkDuplicates REMOVE_DUPLICATES=true MAX_FILE_HANDLES=800 VALIDATION_STRINGENCY=LENIENT I=./06_filtered/2LF4.IP.bam O=./06_markdup/2LF4.IP.markdup.bam M=....
和samtools一些功能类似,着重看下markdup功能,及去除重复 Usage:sambamba-markdup[options][[...]]By default,marks the duplicates without removing them Options:-r,--remove-duplicates remove duplicates instead of just marking them-t,--nthreads=NTHREADS number of threads to use-l,--compression-level=N ...