Sambamba 快速去除PCR重复

改软件可快速去除PCR重复，较samtools，picard更快

安装

点击下载后，减压缩即可
http://lomereiter.github.io/sambamba/docs/sambamba-markdup.html

简单应用

参数

Usage: sambamba [command] [args...]

  Available commands:

    view        view contents and convert from one format
                to another (SAM/BAM/JSON/UNPACK)
    index       build index (BAI)
    merge       merge files (BAM)
    sort        sort file (BAM)
    slice       slice file (BAM using BED)
    markdup     mark or remove duplicates (BAM)
    subsample   subsample (BAM)
    flagstat    output statistics (BAM)
    depth       output statistics (BAM)
    validate    simple validator (BAM)

和samtools一些功能类似，着重看下markdup功能，及去除重复

Usage: sambamba-markdup [options] <input.bam> [<input2.bam> [...]] <output.bam>
       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
                    specify compression level of the resulting file (from 0 to 9)
         -p, --show-progress
                    show progressbar in STDERR
         --tmpdir=TMPDIR
                    specify directory for temporary files

应用也较为简单，可以通过‘-r’参数，设置标记该重复或者去除该重复