官方github：https://github.com/PapenfussLab/gridss/blob/master/QuickStart.md
参考文件下载：
PON文件：https://www.bcgsc.ca/downloads/morinlab/hmftools-references/gridss/pon/ (需要把 gridss_pon_breakpoint.hg38.bedpe 和 gridss_pon_single_breakend.hg38.bed改为gridss_pon_breakpoint.bedpe，gridss_pon_single_breakend.bed 才能用)
conda安装后需额外下载的jar文件：https://github.com/PapenfussLab/GRIDSS/releases
blacklist bed: https://github.com/PapenfussLab/gridss/tree/master/example
批量运行脚本：
perl -ne 'chomp; next if /^$/; @a = split /\t/; print "gridss -r /home/zhoukaiwen/database/gridss/genecode_GRCh38.p14.genome.fa -w $a[0].work -j /home/zhoukaiwen/software/gridss-2.13.2-gridss-jar-with-dependencies.jar -o $a[0].somatic.vcf -b /home/zhoukaiwen/database/gridss/ENCFF356LFX.bed -t 4 ../align/$a[1]_bqsr.bam ../align/$a[0]_bqsr.bam > log/$a[0].log 2>&1 && gridss_somatic_filter --pondir /home/zhoukaiwen/database/gridss/pondir_hg38/ --input $a[0].somatic.vcf --output $a[0].high_confidence_somatic.vcf --fulloutput $a[0].high_and_low_confidence_somatic.vcf --scriptdir \$(dirname\$(which gridss_somatic_filter)) -n 1 -t 2 >> log/$a[0].log 2>&1 && echo $a[0] gridss ok\n";' ../mutect2/sample_pair.txt > RunGridss2.sh
nohup bash -c "cat RunGridss2.sh | parallel -j 4" > log/gridss.log 2>&1 &