rustynuc

根据比对特征计算 8-oxoG 损伤可能性的工具。

安装

Conda

使用 conda 安装

conda install -c bioconda rustynuc

二进制文件

以下提供了预编译的二进制文件

TAR	TAR
ZIP	ZIP

Cargo

如果您已安装 cargo 或已安装 RUSTUP，可以直接从以下位置安装：

• Crates.io

cargo install rustynuc

• Github

cargo install --git https://github.com/bjohnnyd/rustynuc

构建

要从源代码编译，需要 rustup，并且可以从 这里 获取。安装后，下载发行版存档文件并构建。

git clone https://github.com/bjohnnyd/rustynuc.git && cd rustynuc && cargo build --release

所有发行版及其相关的二进制文件和存档都可以在 发行版 下访问。

用法

./rustynuc -h

rustynuc 0.3.0

USAGE:
    rustynuc [FLAGS] [OPTIONS] <bam>

FLAGS:
    -a, --all                Whether to process and print information for every position in the BAM file
    -h, --help               Prints help information
        --no-overlapping     Do not count overlapping mates when calculating total depth
    -n, --no-qval            Skip calculating qvalue
    -p, --pseudocount        Whether to use pseudocounts (increments all counts by 1) when calculating statistics
        --skip-fishers       Skip applying Fisher's Exact Filter on VCF
    -V, --version            Prints version information
    -v, --verbosity          Determines verbosity of the processing, can be specified multiple times -vvv
    -w, --with-track-line    Include track line (for correct visualization with IGV)

OPTIONS:
        --af-both-pass <af-both-pass>        AF on both the ff and fr at which point a call in the VCF will excluded
                                             from the OxoAF filter [default: 0.1]
        --af-either-pass <af-either-pass>    AF above this cutoff in EITHER read orientation will be excluded from OxoAF
                                             filter [default: 0.25]
        --alpha <alpha>                      FDR threshold [default: 0.2]
    -b, --bcf <bcf>                          BCF/VCF for variants called on the supplied alignment file
        --bed <bed>                          A BED file to restrict analysis to specific regions
        --fishers-sig <fishers-sig>          Significance threshold for Fisher's test [default: 0.05]
        --max-depth <max-depth>              Maximum pileup depth to use [default: 1000]
    -m, --min-reads <min-reads>              Minimum number of aligned reads in ff or fr orientation for a position to
                                             be considered [default: 4]
    -q, --quality <quality>                  Minimum base quality to consider [default: 20]
    -r, --reference <reference>              Optional reference which will be used to determine sequence context and
                                             type of change
    -t, --threads <threads>                  Number of threads [default: 4]

ARGS:
    <bam>    Alignments to investigate for possible 8-oxoG damage

输出

默认输出（如果没有提供 --bcf/-b）是一个包含以下信息的 BED 文件：

1. Chromosome
2. Start
3. End
4. Name (format is `<chromosome>_<start>_<end>` or if reference is provided `<chromosome>_<base>_<start>_<end>`
5. -log10 of p-value (p-value is the smallest of the A/C and G/T )
6. Strand
7. Depth
8. Adenine FF:FR counts
9. Cytosine FF:FR counts
10. Guanine FF:FR counts
11. Thymine FF:FR counts
12. A/C two-sided p-value Fisher's Exact Test
13. G/T two-sided p-value Fisher's Exact Test
(14). Sequnce Context (if reference provided)
14/15. adj. pvalue
15/16. Significant at set FDR value (1 if yes, 0 if not)

要仅获取 p 值小于 0.05 的位置

rustynuc -r tests/input/ref.fa.gz tests/alignments/oxog.bam | awk '$12 < 0.05 || $13 < 0.05'  | gzip > sig.bed.gz

如果提供了 VCF/BCF，则输出将以 VCF 格式。VCF 文件中提供了多个摘要

AF_FF_FR 可以用于根据 FF 或 FR 方向上的 AF 过滤。

对于每个等位基因，提供了两个等位频率（AF），例如，要过滤第一个替代位点，可以使用 AF_FF_FR[0] 和 AF_FF_FR[1]。下面的命令将使用 FF/FR 上的 AF 进行过滤，并且 FILTER=="PASS" 确保只有具有 p-val < 0.05 的位点被返回。

FILTERCMD='TYPE =="snp" && AF > 0.04 && FILTER=="PASS" && (FF_FR_AF=="." || (FF_FR_AF[0] >= 0.04 && FF_FR_AF[1] >= 0.04))'
rustynuc --pseudocounts -r tests/input/ref.fa.gz --b tests/input/oxog.vcf.gz tests/alignments/oxog.bam | bcftools filter -Oz -i "$FILTERCMD" > nonoxog.vcf.gz