1、安装 vep
我是通过conda安装到 /jupyter/bioinfo/, vep可执行文件是在/jupyter/bioinfo/share/ensembl-vep-95.2-0
2、用vcf2maf批量转成maf， 这里我使用的是mutect2生成的somatic vcf，注意--vep-path, --vep-data两个参数分别是vep安装的目录和数据所在目录
vcf2maf_cmd = "perl /jupyter/bioinfo/vcf2maf/vcf2maf.pl \
--input-vcf {mutect2_vcf} \
--output-maf {mutect2_maf} \
--ref-fasta /mnt/bioinfo/bundle/hg38/Homo_sapiens_assembly38.fasta.gz \
--vep-path /jupyter/bioinfo/share/ensembl-vep-95.2-0 \
--vep-data /jupyter/bioinfo/bundle/vep \
--filter-vcf /mnt/bioinfo/ExAC/ExAC_nonTCGA.r0.3.1.sites.vep.vcf.gz \
--ncbi-build GRCh38 \
--tumor-id {IDtumor} \
--normal-id {IDnormal}".format(mutect2_vcf = mutect2_vcf, mutect2_maf = mutect2_maf, IDnormal = IDnormal, IDtumor = IDtumor)
- 先生成maf首行，然后append
cat vcf2maf/*.maf | egrep "^#|^Hugo_Symbol" | head -2 > allsamples.vep.maf
cat vcf2maf/*.maf | egrep -v "^#|^Hugo_Symbol" >> allsamples.vep.maf
- 用 maftools分析
