tools for ANNOVAR
Project description
ANNOVAR tools
该包是配合ANNOVAR 对相关文件进行处理的工具集
vcf
将ANNOVAR输入文件,AVinput文件转换为VCF4.0格式
- -i/--avinput: 输入文件,AVinput格式
- -r/--reference: 参考基因组文件如hg19.fa,请事先使用samtools faidex构建索引
- -o/--vcf: 输出的VCF文件
zhuy@ubuntu:/projects/example$ annovar_tools.py vcf -i test.avinput -r hg19.fa -o test.vcf
split
将ANNOVAR注释结果按照Gene拆分为多行,一次只能拆分一种gene-based数据库
- -i/--avoutput: 输入文件,ANNVOAR注释结果,如test.hg19_multianno.txt
- -r/--refgenes: 运行ANNOVAR所用的注释refGene文件,如hg19_ensGene.txt,hg19_knownGene.txt,hg19_refGeneWithVer.txt
- -g/gene_db: 所需拆分的gene-based数据库, 如refGeneWithVer,即ANNVOAR g参数对应的数据库名称,在ANNOVAR结果中体现为"Func.refGeneWithVer, Gene.refGeneWithVer, GeneDetail.refGeneWithVer, ExonicFunc.refGeneWithVer, AAChange.refGeneWithVer"
- -o/--outfile: 输出的拆分后的文件
zhuy@ubuntu:/projects/example$ annovar_tools.py split \
-i test.hg19_multianno.txt \
-r hg19_refGeneWithVer.txt \
-r hg19_ensGene.txt \
-r hg19_knownGene.txt \
-g refGeneWithVer
-o test.hg19_multianno.refGeneWithVer.txt
Project details
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
annovar_tools-0.0.2.tar.gz
(4.8 kB
view hashes)
Built Distribution
Close
Hashes for annovar_tools-0.0.2-py3-none-any.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 1ef160a8ad0860279f22ab69625e41cbe75d022a75f1ec6b4f7ada8f6e8b13ce |
|
MD5 | befaa73ea207feb71d0ee8da704777c0 |
|
BLAKE2b-256 | 073867283a731db5375eb3d7d788f3af03a30b8c628f54a2024ad0fa61a38b5a |