gatk中的 GenomicsDBImport 模块
官网:https://gatk.broadinstitute.org/hc/en-us/articles/5358869876891-GenomicsDBImport
001、一般用法,变异检测库
gatk --java-options "-Xmx4g -Xms4g" GenomicsDBImport -V SRR21814509.g.vcf -V SRR21814514.g.vcf --genomicsdb-workspace-path my_database --tmp-dir /public/home/b20223040323/tmp -L NC_003070.9
002、-L参数可以指定多条染色体
gatk --java-options "-Xmx4g -Xms4g" GenomicsDBImport -V SRR21814509.g.vcf -V SRR21814514.g.vcf --genomicsdb-workspace-path my_database --tmp-dir /public/home/b20223040323/tmp -L chr.list
chr.list 格式:
NC_003070.9 NC_003071.7
003、将g.vcf文件写入文件列表
gatk --java-options "-Xmx4g -Xms4g" GenomicsDBImport --sample-name-map cohort.sample_map --genomicsdb-workspace-path my_database --tmp-dir /public/home/b20223040323/tmp -L NC_003070.9
cohort.sample_map 文件格式:
SRR21814509 SRR21814509.g.vcf
SRR21814514 SRR21814514.g.vcf
004、添加样本,更新my_database数据库
gatk GenomicsDBImport -V SRR21814498.g.vcf --genomicsdb-update-workspace-path my_database --tmp-dir /public/home/b20223040323/tmp
005、从数据集中对单条染色体进行变异检测
gatk --java-options "-Xmx60G -XX:+UseParallelGC -XX:ParallelGCThreads=20" GenotypeGVCFs -R /public/home/b20223040323/arabidopsis/fasta/GCF_000001735.4_TAIR10.1_genomic.fna -L NC_003070.9 -V gendb://my_database -O test.vcf
006、对单条染色体的指定范围进行变异检测
gatk --java-options "-Xmx60G -XX:+UseParallelGC -XX:ParallelGCThreads=20" GenotypeGVCFs -R /public/home/b20223040323/arabidopsis/fasta/GCF_000001735.4_TAIR10.1_genomic.fna -L NC_003070.9:1-1000 -V gendb://my_database -O test.vcf
参考:
01、https://gatk.broadinstitute.org/hc/en-us/articles/360047216891-GenomicsDBImport