原文：https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-021-03995-y
github：https://github.com/cpwardell/FiNGS
安装
conda create -n fings python=3.7
conda activate fings
conda install fings
# Locate the FiNGS package, navigate to the example data and run the script to confirm your installation is correct.
## Navigate to this directory /path/to/conda/envs/fings/lib/python3.7/site-packages/fings/exampledata/
./test.sh
运行
# 构建批量运行脚本
perl -ne 'chomp; next if /^$/; @a = split /\t/; print "fings -t ../align/$a[0]_bqsr.bam -n ../align/$a[1]_bqsr.bam -v $a[0].somatic.passed.vcf --PASSonlyin --PASSonlyout -d $a[0]_FiNGS -j 4 && echo $a[0] FiNGS ok\n"' sample_pair.txt > RunFiNGS.sh突变注释
perl -ne 'chomp;next if($_=~/^$/);my @a=split /\t/;print "vcf2maf.pl --input-vcf $a[0].somatic.passed.filtered.vcf --output-maf $a[0].FiNGS.maf --normal-id $a[1] --tumor-id $a[0] --vcf-tumor-id $a[0] --vcf-normal-id $a[1] --vep-path /home/zhoukaiwen/software/anaconda3/envs/vcf2maf/bin --vep-data /home/zhoukaiwen/database/vep/ --ref-fasta /home/zhoukaiwen/database/GRCh38/genecode_GRCh38.p14.genome.fa --verbose --ncbi-build GRCh38 --cache-version 114 && echo $a[0] vcf2maf ok\n"' ../sample_pair.txt >vcf2maf.sh