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用Annovar注释人类以外的基因组

2022-06-08 10:55阅读：

http://blog.sina.cn/dpool/blog/u/1910449537

一、以大肠杆菌为例，构建所需注释所需文件 1，下载gtf或者gff文件。
wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/022/665/GCF_000022665.1_ASM2266v1/GCF_000022665.1_ASM2266v1_genomic.gff.gz .
wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/022/665/GCF_000022665.1_ASM2266v1/GCF_000022665.1_ASM2266v1_genomic.gtf.gz .
2，新建注释文件夹
mkdir ECdb
3，解压文件
gunzip GCF_000022665.1_ASM2266v1_genomic.gff.gz
4，下载gff3ToGenePred’ 或gtfToGenePred 工具，推荐使用GTF格式，因为有些GFF3格式文件转换可能不正确
wget http://hgdownload.soe.ucsc.edu/admin/exe/lin
ux.x86_64/gtfToGenePred .
wget http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/gff3ToGenePred .
chmod +x gff3ToGenePred
5，生成GenePred文件
./gtfToGenePred -genePredExt GCF_000022665.1_ASM2266v1_genomic.gtf EC_refGene.txt
./gff3ToGenePred GCF_000022665.1_ASM2266v1_genomic.gff EC_refGene.txt -useName
哪个格式对用哪个
6，下载基因组文件
wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/022/665/GCF_000022665.1_ASM2266v1/GCF_000022665.1_ASM2266v1_genomic.fna.gz .
gunzip GCF_000022665.1_ASM2266v1_genomic.fna.gz
mv GCF_000022665.1_ASM2266v1_genomic.fna GCF_000022665.1_ASM2266v1_genomic.dna.fa
7，用 retrieve_seq_from_fasta.pl生成 transcript FASTA file
perl /apps/annovar/retrieve_seq_from_fasta.pl --format refGene --seqfile GCF_000022665.1_ASM2266v1_genomic.dna.fa EC_refGene.txt --outfile EC_refGeneMrna.fa
8，注释
perl /apps/annovar/table_annovar.pl LDTYF06_323.raw.variant.vcf.gz ECdb -buildver EC -out test -remove -protocol refGene -operation g -nastring . -vcfinput --dot2underline

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