Clara Parabricks v4.4.0

HaplotypeCaller 教程

本教程将向您展示如何运行黄金标准的 GATK 变异调用器 HaplotypeCaller,它将采用来自 FQ2BAM 教程的对齐输出 BAM,从活跃区域组装合理的单倍型,并根据贝叶斯规则识别基因型似然性。结果是一个变异调用格式 (VCF) 文件,其中包含基因组中所有变异调用的信息,包括它们在基因组中的位置和等位基因信息。

要执行此操作,请运行以下命令

复制
已复制!
            

$ docker run \ --gpus all \ --rm \ --volume $(pwd):/workdir \ --volume $(pwd):/outputdir \ nvcr.io/nvidia/clara/clara-parabricks:4.4.0-1 \ pbrun haplotypecaller \ --ref /workdir/parabricks_sample/Ref/Homo_sapiens_assembly38.fasta \ --in-bam /workdir/fq2bam_output.bam \ --out-variants /outputdir/variants.vcf [PB Info 2022-Sep-02 20:08:13] ------------------------------------------------------------------------------ [PB Info 2022-Sep-02 20:08:13] || Parabricks accelerated Genomics Pipeline || [PB Info 2022-Sep-02 20:08:13] || Version 4.0.0-1 || [PB Info 2022-Sep-02 20:08:13] || GPU-GATK4 HaplotypeCaller || [PB Info 2022-Sep-02 20:08:13] ------------------------------------------------------------------------------ [PB Info 2022-Sep-02 20:08:48] 0 /outputdir/fq2bam_output.bam/outputdir/variants.vcf [PB Info 2022-Sep-02 20:08:48] ProgressMeter - Current-Locus Elapsed-Minutes Regions-Processed Regions/Minute [PB Info 2022-Sep-02 20:08:58] chr1:26179201 0.2 143431 860586 [PB Info 2022-Sep-02 20:09:08] chr1:88982401 0.3 428734 1286202 [PB Info 2022-Sep-02 20:09:18] chr1:155342401 0.5 622031 1244062 [PB Info 2022-Sep-02 20:09:28] chr1:222508801 0.7 921183 1381774 [PB Info 2022-Sep-02 20:09:38] chr2:38697601 0.8 1206544 1447852 [PB Info 2022-Sep-02 20:09:48] chr2:101697601 1.0 1469587 1469585 [PB Info 2022-Sep-02 20:09:58] chr2:176107201 1.2 1802198 1544741 [PB Info 2022-Sep-02 20:10:08] chr3:8990401 1.3 2124644 1593483 [PB Info 2022-Sep-02 20:10:18] chr3:55473601 1.5 2349628 1566418 [PB Info 2022-Sep-02 20:10:28] chr3:133680001 1.7 2671435 1602861 [PB Info 2022-Sep-02 20:10:38] chr3:192724801 1.8 2922628 1594160 [PB Info 2022-Sep-02 20:10:48] chr4:61934401 2.0 3222268 1611134 [PB Info 2022-Sep-02 20:10:58] chr4:143524801 2.2 3573491 1649303 [PB Info 2022-Sep-02 20:11:08] chr5:38947201 2.3 3949926 1692825 [PB Info 2022-Sep-02 20:11:18] chr5:116337601 2.5 4255653 1702261 [PB Info 2022-Sep-02 20:11:28] chr5:176035201 2.7 4508018 1690506 [PB Info 2022-Sep-02 20:11:38] chr6:54768001 2.8 4780747 1687322 [PB Info 2022-Sep-02 20:11:48] chr6:152140801 3.0 5176363 1725454 [PB Info 2022-Sep-02 20:11:58] chr7:27105601 3.2 5377117 1698036 [PB Info 2022-Sep-02 20:12:08] chr7:105105601 3.3 5713863 1714158 [PB Info 2022-Sep-02 20:12:18] chr8:18086401 3.5 6002114 1714889 [PB Info 2022-Sep-02 20:12:28] chr8:73915201 3.7 6267992 1709451 [PB Info 2022-Sep-02 20:12:38] chr9:5553601 3.8 6588617 1718769 [PB Info 2022-Sep-02 20:12:48] chr9:93672001 4.0 6886981 1721745 [PB Info 2022-Sep-02 20:12:58] chr10:4094401 4.2 7095584 1702939 [PB Info 2022-Sep-02 20:13:08] chr10:94593601 4.3 7489282 1728295 [PB Info 2022-Sep-02 20:13:18] chr11:18398401 4.5 7757420 1723871 [PB Info 2022-Sep-02 20:13:28] chr11:95976001 4.7 8083942 1732273 [PB Info 2022-Sep-02 20:13:38] chr12:6652801 4.8 8282324 1713584 [PB Info 2022-Sep-02 20:13:48] chr12:70632001 5.0 8560282 1712056 [PB Info 2022-Sep-02 20:13:58] chr13:24446401 5.2 8860588 1714952 [PB Info 2022-Sep-02 20:14:08] chr13:99038401 5.3 9200934 1725175 [PB Info 2022-Sep-02 20:14:18] chr14:68467201 5.5 9480546 1723735 [PB Info 2022-Sep-02 20:14:28] chr15:66432001 5.7 9821985 1733291 [PB Info 2022-Sep-02 20:14:38] chr16:31128001 5.8 10123582 1735471 [PB Info 2022-Sep-02 20:14:48] chr17:15782401 6.0 10402640 1733773 [PB Info 2022-Sep-02 20:14:58] chr17:55262401 6.2 10553414 1711364 [PB Info 2022-Sep-02 20:15:08] chr18:27960001 6.3 10790487 1703761 [PB Info 2022-Sep-02 20:15:18] chr19:15883201 6.5 11074759 1703809 [PB Info 2022-Sep-02 20:15:28] chr20:16108801 6.7 11311965 1696794 [PB Info 2022-Sep-02 20:15:38] chr21:10468801 6.8 11563626 1692237 [PB Info 2022-Sep-02 20:15:48] chr22:29289601 7.0 11766272 1680896 [PB Info 2022-Sep-02 20:15:58] chrX:77452801 7.2 12197330 1701952 [PB Info 2022-Sep-02 20:16:08] chrUn_JTFH01000876v1_decoy:1 7.3 12604293 1718767 [PB Info 2022-Sep-02 20:16:18] Total time taken: 450.258102 [PB Info 2022-Sep-02 20:16:18] ------------------------------------------------------------------------------ [PB Info 2022-Sep-02 20:16:18] || Program: GPU-GATK4 HaplotypeCaller || [PB Info 2022-Sep-02 20:16:18] || Version: 4.0.0-1 || [PB Info 2022-Sep-02 20:16:18] || Start Time: Fri Sep 2 20:08:13 2022 || [PB Info 2022-Sep-02 20:16:18] || End Time: Fri Sep 2 20:16:18 2022 || [PB Info 2022-Sep-02 20:16:18] || Total Time: 8 minutes 5 seconds || [PB Info 2022-Sep-02 20:16:18] ------------------------------------------------------------------------------ /usr/local/parabricks/binaries//bin/htvc /workdir/parabricks_sample/Ref/Homo_sapiens_assembly38.fasta /outputdir/fq2bam_output.bam 1 -o /outputdir/variants.vcf -nt 5 Please visit https://docs.nvda.net.cn/clara/#parabricks for detailed documentation

如果您遇到内存不足错误,请确保您的计算机有足够的 RAM,并且没有其他程序占用大量内存。

您现在应该在您的目录中拥有以下文件

复制
已复制!
            

$ ls -lrt -rw-r--r-- 1 root root 4819386804 Sep 2 15:58 fq2bam_output.bam -rw-r--r-- 1 root root 6882792 Sep 2 15:59 fq2bam_output.bam.bai -rw-r--r-- 1 root root 87690 Sep 2 15:59 fq2bam_output_chrs.txt -rw-r--r-- 1 root root 23643404 Sep 2 16:16 variants.vcf (sample data not shown)

variants.vcf 的前十行非标题行应如下所示

复制
已复制!
            

chr1 16378 . T C 45.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=23.55;QD=22.64;SOR=2.303 GT:AD:DP:GQ:PL 1/1:0,2:2:6:57,6,0 chr1 63268 . T C 43.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=23.09;QD=21.64;SOR=2.303 GT:AD:DP:GQ:PL 1/1:0,2:2:6:55,6,0 chr1 63516 . A G 1202.03 . AC=2;AF=1.00;AN=2;DP=40;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=26.22;QD=30.05;SOR=1.292 GT:AD:DP:GQ:PL 1/1:0,40:40:99:1216,120,0 chr1 63527 . T C 1002.03 . AC=2;AF=1.00;AN=2;DP=33;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=26.05;QD=30.36;SOR=1.179 GT:AD:DP:GQ:PL 1/1:0,33:33:99:1016,99,0 chr1 131609 . C A 83.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.275;DP=11;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=20.00;MQRankSum=0.000;QD=7.60;ReadPosRankSum=-1.349;SOR=0.551 GT:AD:DP:GQ:PL 0/1:6,5:11:91:91,0,115 chr1 133483 . G T 70.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.534;DP=8;ExcessHet=3.0103;FS=3.332;MLEAC=1;MLEAF=0.500;MQ=26.65;MQRankSum=1.611;QD=8.83;ReadPosRankSum=-0.703;SOR=2.303 GT:AD:DP:GQ:PL 0/1:5,3:8:78:78,0,100 chr1 264627 . A G 37.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=49.00;QD=18.64;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 chr1 268012 . G A 330.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.636;DP=116;ExcessHet=3.0103;FS=1.639;MLEAC=1;MLEAF=0.500;MQ=39.33;MQRankSum=-6.168;QD=2.85;ReadPosRankSum=-1.358;SOR=0.895 GT:AD:DP:GQ:PL 0/1:93,23:116:99:338,0,3307 chr1 268130 . G T 2188.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.543;DP=228;ExcessHet=3.0103;FS=8.632;MLEAC=1;MLEAF=0.500;MQ=44.88;MQRankSum=-12.533;QD=9.60;ReadPosRankSum=1.105;SOR=0.356 GT:AD:DP:GQ:PL 0/1:128,100:228:99:2196,0,4482 chr1 268516 . C T 59.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.465;DP=7;ExcessHet=3.0103;FS=3.680;MLEAC=1;MLEAF=0.500;MQ=52.18;MQRankSum=-0.180;QD=8.51;ReadPosRankSum=-0.366;SOR=2.258 GT:AD:DP:GQ:PL 0/1:5,2:7:67:67,0,138

上一篇 FQ2BAM 教程
下一篇 云使用指南
© 版权所有 2025,Nvidia。 上次更新于 2025 年 1 月 13 日。