把vcf文件转换为maf格式，肿瘤外显子上游分析教程到此为止

cd ~/biosoft/vcf2maf/
export VCF2MAF_URL=`curl -sL https://api.github.com/repos/mskcc/vcf2maf/releases | grep -m1 tarball_url | cut -d\" -f4`
curl -L -o mskcc-vcf2maf.tar.gz $VCF2MAF_URL; tar -zxf mskcc-vcf2maf.tar.gz; cd mskcc-vcf2maf-*
mv * ../ 
perl ~/biosoft/vcf2maf/vcf2maf.pl --man 

[jianmingzeng@jade mskcc-vcf2maf-747a1bb]$ perl vcf2maf.pl  --help
Usage:
     perl vcf2maf.pl --help
     perl vcf2maf.pl --input-vcf WD4086.vcf --output-maf WD4086.maf --tumor-id WD4086 --normal-id NB4086
Options:
     --input-vcf      Path to input file in VCF format
     --output-maf     Path to output MAF file
     --tmp-dir        Folder to retain intermediate VCFs after runtime [Default: Folder containing input VCF]
     --tumor-id       Tumor_Sample_Barcode to report in the MAF [TUMOR]
     --normal-id      Matched_Norm_Sample_Barcode to report in the MAF [NORMAL]
     --vcf-tumor-id   Tumor sample ID used in VCF's genotype columns [--tumor-id]
     --vcf-normal-id  Matched normal ID used in VCF's genotype columns [--normal-id]
     --custom-enst    List of custom ENST IDs that override canonical selection
     --vep-path       Folder containing the vep script [~/vep]
     --vep-data       VEP's base cache/plugin directory [~/.vep]
     --vep-forks      Number of forked processes to use when running VEP [4]
     --buffer-size    Number of variants VEP loads at a time; Reduce this for low memory systems [5000]
     --any-allele     When reporting co-located variants, allow mismatched variant alleles too
     --ref-fasta      Reference FASTA file [~/.vep/homo_sapiens/91_GRCh37/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa.gz]
     --filter-vcf     A VCF for FILTER tag common_variant. Set to 0 to disable [~/.vep/ExAC_nonTCGA.r0.3.1.sites.vep.vcf.gz]
     --max-filter-ac  Use tag common_variant if the filter-vcf reports a subpopulation AC higher than this [10]
     --species        Ensembl-friendly name of species (e.g. mus_musculus for mouse) [homo_sapiens]
     --ncbi-build     NCBI reference assembly of variants MAF (e.g. GRCm38 for mouse) [GRCh37]
     --cache-version  Version of offline cache to use with VEP (e.g. 75, 84, 91) [Default: Installed version]
     --maf-center     Variant calling center to report in MAF [.]
     --retain-info    Comma-delimited names of INFO fields to retain as extra columns in MAF []
     --min-hom-vaf    If GT undefined in VCF, minimum allele fraction to call a variant homozygous [0.7]
     --remap-chain    Chain file to remap variants to a different assembly before running VEP
     --help           Print a brief help message and quit
     --man            Print the detailed manual

## 自己单独运行VEP，注释速度很慢
# Processed 1969 total variants (9 vars/sec, 9 vars/sec total)
perl ~/vep/variant_effect_predictor.pl  -i somatic.vcf  -o test.vcf  \
--cache --force_overwrite  --assembly GRCh38 --vcf
# 看起来上面的VEP完全没有必要运行

# 一步到位，包括VEP和 vcf2maf，而且注释非常快,因为调用了5个线程
# Processed 1969 total variants (53 vars/sec, 53 vars/sec total)
 perl ~/biosoft/vcf2maf/vcf2maf.pl --input-vcf somatic.vcf   --output-maf test.maf  \
 --ref-fasta ~/.vep/homo_sapiens/86_GRCh38/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz \
 --tumor-id 1092NTT  --normal-id  1257NT --ncbi-build GRCh38

for i in  *filter.vcf ;
do
echo $i
j=$(basename "$i" _filter.vcf )
echo ${j^^}
perl ~/biosoft/vcf2maf/vcf2maf.pl --input-vcf $i   --output-maf ${j^^}.maf  \
--ref-fasta ~/.vep/homo_sapiens/86_GRCh38/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz \
--tumor-id  ${j^^}_T  --normal-id ${j^^}_N --ncbi-build GRCh38
done 

1.3M May 30 14:00 OSCC_01.maf
745K May 30 14:01 OSCC_04.maf
576K May 30 14:01 OSCC_06.maf
730K May 30 14:02 OSCC_09.maf