samtools软件的安装及用法

samtools是一个用于操作sam和bam文件的工具合集。能够实现二进制查看、格式转换、排序及合并等功能，结合sam格式中的flag、tag等信息，还可以完成比对结果的统计汇总。

- samtools安装

conda install -c bioconda samtools  # 参考：https://anaconda.org/bioconda/samtools
samtools --help  # 安装完即可使用
#安装路径：/export/home/hushy/miniconda2/pkgs/samtools-1.9-h8571acd_11

- samtools用法

Usage:   samtools <command> [options]
Commands:
  -- Indexing
     dict           create a sequence dictionary file
     faidx          index/extract FASTA
     fqidx          index/extract FASTQ
     index          index alignment
  -- Editing
     calmd          recalculate MD/NM tags and '=' bases
     fixmate        fix mate information
     reheader       replace BAM header
     targetcut      cut fosmid regions (for fosmid pool only)
     addreplacerg   adds or replaces RG tags
     markdup        mark duplicates
  -- File operations
     collate        shuffle and group alignments by name
     cat            concatenate BAMs
     merge          merge sorted alignments
     mpileup        multi-way pileup
     sort           sort alignment file
     split          splits a file by read group
     quickcheck     quickly check if SAM/BAM/CRAM file appears intact
     fastq          converts a BAM to a FASTQ
     fasta          converts a BAM to a FASTA
  -- Statistics
     bedcov         read depth per BED region
     depth          compute the depth
     flagstat       simple stats
     idxstats       BAM index stats
     phase          phase heterozygotes
     stats          generate stats (former bamcheck)
  -- Viewing
     flags          explain BAM flags
     tview          text alignment viewer
     view           SAM<->BAM<->CRAM conversion
     depad          convert padded BAM to unpadded BAM