生信工具推荐之(3) perbase

Per-base per-nucleotide depth analysis

统计bam文件每个位置的测序深度、和各种碱基深度、还包括indel，支持多线程。

github：

https://github.com/sstadick/perbase.git

install:

conda install -c bioconda perbase
# OR
cargo install perbase

help:

perbase 0.9.0
Seth Stadick <sstadick@gmail.com>
Fast and correct perbase BAM/CRAM analysis.

USAGE:
    perbase <SUBCOMMAND>

FLAGS:
    -h, --help       Prints help information
    -V, --version    Prints version information

SUBCOMMANDS:
    base-depth        Calculate the depth at each base, per-nucleotide
    help              Prints this message or the help of the given subcommand(s)
    merge-adjacent    Merge adjacent intervals that have the same depth. Input must be sorted like: `sort -k1,1
                      -k2,2n in.bed > in.sorted.bed`
    only-depth        Calculate the only the depth at each base

Example ouput:

REF     POS     REF_BASE        DEPTH   A       C       G       T       N       INS     DEL     REF_SKIP        FAIL    NEAR_MAX_DEPTH
chr1    709636  T       16      0       0       0       16      0       0       0       0       0   false
chr1    709637  T       16      0       4       0       12      0       0       0       0       0   false
chr1    709638  A       16      16      0       0       0       0       0       0       0       0   false
chr1    709639  G       16      0       0       16      0       0       0       0       0       0   false
chr1    709640  A       16      16      0       0       0       0       0       0       0       0   false
chr1    709641  A       16      16      0       0       0       0       0       0       0       0   false
chr1    709642  G       16      0       0       16      0       0       0       0       0       0   false
chr1    709643  G       16      0       0       16      0       0       0       0       0       0   false
chr1    709644  T       16      0       0       0       16      0       0       0       0       0   false
chr1    709645  G       16      0       0       16      0       0       0       0       0       0   false