{"id":66381,"date":"2026-11-06T09:07:55","date_gmt":"2026-11-06T01:07:55","guid":{"rendered":"https:\/\/www.biocloudservice.com\/wordpress\/?p=66381"},"modified":"2026-11-06T09:07:55","modified_gmt":"2026-11-06T01:07:55","slug":"clair3-gpu-long-read-wgs-variant-calling","status":"publish","type":"post","link":"https:\/\/www.biocloudservice.com\/wordpress\/clair3-gpu-long-read-wgs-variant-calling\/","title":{"rendered":"30\u00d7\u957f\u8bfb\u957f\u5168\u57fa\u56e0\u7ec412\u201420\u5206\u949f\uff1aClair3 GPU\u771f\u6b63\u9700\u8981\u7684\uff0c\u4e0d\u53ea\u662f\u4e00\u5f20\u663e\u5361"},"content":{"rendered":"
\n

\u4e00\u4efd30\u00d7\u4eba\u7c7b\u957f\u8bfb\u957f\u5168\u57fa\u56e0\u7ec4BAM\u5e38\u5e38\u8fbe\u5230\u6570\u767eGB\u3002\u628a\u5b83\u4ea4\u7ed9\u6df1\u5ea6\u5b66\u4e60\u53d8\u5f02\u68c0\u6d4b\u5de5\u5177\u540e\uff0c\u5f88\u591a\u56e2\u961f\u4f1a\u53d1\u73b0\uff1aGPU\u5df2\u7ecf\u4e70\u4e86\uff0c\u6d41\u7a0b\u5374\u4ecd\u7136\u5361\u5728\u7279\u5f81\u751f\u6210\u3001\u5206\u76f8\u3001BAM\u53cd\u590d\u8bfb\u5199\u6216CPU\u7ebf\u7a0b\u4e0d\u591f\u3002GPU\u5229\u7528\u7387\u5ffd\u9ad8\u5ffd\u4f4e\uff0c\u8f93\u51fa\u76ee\u5f55\u6301\u7eed\u81a8\u80c0\uff0c\u6700\u540e\u5f97\u5230\u7684VCF\u8fd8\u53ef\u80fd\u56e0\u4e3a\u6a21\u578b\u548c\u6d4b\u5e8f\u5316\u5b66\u7248\u672c\u4e0d\u5339\u914d\u800c\u9700\u8981\u91cd\u8dd1\u3002<\/p>\n

2026\u5e74\u53d1\u8868\u4e8e\u300aBioinformatics\u300b\u7684\u52a0\u901f\u7248Clair3\u7ed9\u51fa\u4e86\u4e00\u4e2a\u975e\u5e38\u9192\u76ee\u7684\u7ed3\u679c\uff1a30\u00d7\u957f\u8bfb\u957f\u5168\u57fa\u56e0\u7ec4\u53d8\u5f02\u68c0\u6d4b\uff0c\u572832\u4e2aCPU\u7ebf\u7a0b\u548c\u4e00\u5f20NVIDIA GPU\u4e0a\u53ef\u7528\u7ea612\u201420\u5206\u949f\u5b8c\u6210\uff1b\u8bba\u6587\u6b63\u6587\u4e2d\u7684Linux\u793a\u4f8b\u4f7f\u7528RTX 4090\uff0c\u8fd0\u884c\u7ea620\u5206\u949f\uff0c\u76f8\u6bd4\u521d\u59cb\u7248\u672c\u83b7\u5f97\u7ea610\u201420\u500d\u63d0\u901f\u3002ONT\u4e0ePacBio GIAB HG003 30\u00d7\u6570\u636e\u7684SNP F1\u5206\u522b\u8fbe\u523099.32%\u548c99.70%\u3002\u4f46\u8fd9\u7ec4\u6570\u5b57\u53ea\u6709\u653e\u56de\u7248\u672c\u3001\u786c\u4ef6\u548c\u6570\u636e\u6761\u4ef6\u91cc\u624d\u6709\u610f\u4e49\u3002<\/p>\n

\"Clair3
Clair3 GPU\u8d44\u6e90\u89c4\u5212\uff1a\u8bba\u6587\u57fa\u51c6\u3001\u5f53\u524d\u7248\u672c\u548c\u771f\u5b9e\u9879\u76ee\u94fe\u8def\u5fc5\u987b\u5206\u5f00\u6838\u5bf9\u3002<\/figcaption><\/figure>\n

\u8bba\u6587\u901f\u5ea6\u5f88\u5feb\uff0c\u4f46\u4e0d\u80fd\u76f4\u63a5\u5199\u8fdb\u9879\u76ee\u6392\u671f<\/h2>\n
\n\n\n\n\n\n\n\n\n
\u6838\u5bf9\u9879<\/th>\n2026\u8bba\u6587\u57fa\u51c6<\/th>\n\u5f53\u524d\u5b98\u65b9\u4e3b\u7ebf<\/th>\n\u5bf9\u90e8\u7f72\u7684\u5f71\u54cd<\/th>\n<\/tr>\n<\/thead>\n
\u6df1\u5ea6\u5b66\u4e60\u540e\u7aef<\/td>\nGPU\u5206\u652f\u4f7f\u7528TensorFlow<\/td>\nClair3 v2\u5df2\u8fc1\u79fb\u5230PyTorch<\/td>\nv1\u6a21\u578b\u4e0d\u80fd\u76f4\u63a5\u7ed9v2\u4f7f\u7528<\/td>\n<\/tr>\n
\u5178\u578b\u786c\u4ef6<\/td>\n32\u7ebf\u7a0b\uff0bRTX 4090<\/td>\nNVIDIA GPU\u955c\u50cf\u57fa\u4e8eCUDA 12.1<\/td>\n\u9a71\u52a8\u3001\u5bb9\u5668\u5de5\u5177\u548cGPU\u578b\u53f7\u90fd\u8981\u9a8c\u8bc1<\/td>\n<\/tr>\n
\u5178\u578b\u6570\u636e<\/td>\n30\u00d7 ONT\/PacBio GIAB\u4eba\u7c7b\u5168\u57fa\u56e0\u7ec4<\/td>\n\u652f\u6301ONT\u3001HiFi\u548cIllumina\u6a21\u578b<\/td>\n\u901f\u5ea6\u968f\u8986\u76d6\u5ea6\u3001\u5019\u9009\u6570\u548c\u6a21\u578b\u53d8\u5316<\/td>\n<\/tr>\n
\u5e76\u884c\u7b56\u7565<\/td>\n\u5207\u5757\u3001LongPhase\u3001\u5185\u5b58\u5185haplotag<\/td>\n\u9ed8\u8ba4\u5757\u5927\u5c0f500\u4e07\u78b1\u57fa\uff0c\u53ef\u8c03\u6574<\/td>\nCPU\u3001I\/O\u4e0eGPU\u5fc5\u987b\u534f\u540c\uff0c\u4e0d\u662f\u53ea\u770b\u663e\u5b58<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<\/div>\n

\u8bba\u6587\u62a5\u544a\u7684\u662f\u53ef\u590d\u73b0\u7684\u57fa\u51c6\uff0c\u4e0d\u662f\u6240\u6709\u6837\u672c\u7684\u56fa\u5b9a\u8017\u65f6\u3002\u5f53\u524d\u5b98\u65b9\u4ed3\u5e93\u5df2\u7ecf\u53d1\u5e03Clair3 v2.0.5\uff0c\u5e76\u5b8c\u6210PyTorch\u8fc1\u79fb\uff1b\u65e7TensorFlow\u6a21\u578b\u4e0ev2\u6a21\u578b\u4e0d\u517c\u5bb9\u3002\u82e5\u76f4\u63a5\u62c9\u53d6\u6700\u65b0hkubal\/clair3:gpu<\/code>\u955c\u50cf\uff0c\u5c31\u5e94\u5728\u81ea\u5df1\u7684\u6570\u636e\u548c\u786c\u4ef6\u4e0a\u91cd\u65b0\u6d4b\u65f6\uff0c\u4e0d\u80fd\u628a\u8bba\u6587\u4e2d\u65e7GPU\u5206\u652f\u768420\u5206\u949f\u539f\u6837\u5f53\u4f5c\u4ea4\u4ed8\u627f\u8bfa\u3002<\/p>\n

\u8fd8\u8981\u6ce8\u610f\u8ba1\u65f6\u8fb9\u754c\u3002Clair3\u63a5\u6536\u7684\u662f\u5df2\u7ecf\u6bd4\u5bf9\u3001\u6392\u5e8f\u5e76\u5efa\u7acb\u7d22\u5f15\u7684BAM\u548c\u53c2\u8003FASTA\uff0c\u56e0\u6b64\u201c12\u201420\u5206\u949f\u201d\u4e0d\u5305\u542bDorado basecalling\u3001minimap2\u6bd4\u5bf9\u3001BAM\u6392\u5e8f\u3001\u7d22\u5f15\u3001\u53d8\u5f02\u6ce8\u91ca\u548c\u4eba\u5de5\u89e3\u8bfb\u3002\u5bf9\u4e8e\u539f\u59cbPOD5\u6216FASTQ\u9879\u76ee\uff0c\u524d\u540e\u73af\u8282\u53ef\u80fd\u6bd4\u53d8\u5f02\u8c03\u7528\u672c\u8eab\u66f4\u8017\u65f6\u3002\u670d\u52a1\u5668\u6d4b\u7b97\u5fc5\u987b\u6309\u201c\u539f\u59cb\u4fe1\u53f7\u5230\u53ef\u89e3\u91ca\u7ed3\u679c\u201d\u7684\u5b8c\u6574\u94fe\u8def\u5217\u8d44\u6e90\uff0c\u800c\u4e0d\u662f\u53ea\u62ff\u8bba\u6587\u4e2d\u6700\u5feb\u7684\u4e00\u6bb5\u66ff\u4ee3\u6574\u4e2a\u9879\u76ee\u5468\u671f\u3002<\/p>\n

\u540c\u4e00\u4efd\u6570\u636e\u5728\u4e0d\u540c\u8f93\u51fa\u6a21\u5f0f\u4e0b\u4e5f\u4f1a\u53d8\u6162\u3002\u53ea\u8f93\u51fa\u53d8\u5f02\u4f4d\u70b9\u3001\u751f\u6210GVCF\u3001\u9650\u5236BED\u76ee\u6807\u533a\u95f4\u3001\u542f\u7528\u4fe1\u53f7\u611f\u77e5\u7279\u5f81\u6216\u505a\u6700\u7ec8\u5206\u76f8\uff0c\u5bf9\u5019\u9009\u6570\u91cf\u548c\u8bfb\u5199\u91cf\u7684\u5f71\u54cd\u4e0d\u540c\u3002\u6587\u7ae0\u4e2d\u7684\u901f\u5ea6\u66f4\u9002\u5408\u7528\u6765\u5224\u65adGPU\u52a0\u901f\u7684\u6f5c\u529b\uff0c\u771f\u6b63\u6392\u671f\u4ecd\u5e94\u4ee5\u81ea\u5df1\u7684BAM\u3001\u6a21\u578b\u548c\u53c2\u6570\u505a\u57fa\u7ebf\u3002<\/p>\n

\u4e3a\u4ec0\u4e48\u4e00\u5f20GPU\u4ecd\u53ef\u80fd\u201c\u7b49\u6570\u636e\u201d<\/h2>\n

Clair3\u5148\u7528\u8f7b\u91cfpileup\u6a21\u578b\u5904\u7406\u5927\u591a\u6570\u5019\u9009\uff0c\u518d\u628a\u4e0d\u786e\u5b9a\u533a\u57df\u4ea4\u7ed9\u8ba1\u7b97\u66f4\u91cd\u7684full-alignment\u6a21\u578b\u3002\u52a0\u901f\u7248\u628a\u57fa\u56e0\u7ec4\u5207\u6210\u7ea63\u201410 Mb\u7684\u5c0f\u5757\u5e76\u884c\u751f\u6210\u7279\u5f81\uff0c\u5f15\u5165LongPhase\u8fdb\u884c\u5feb\u901f\u4e2d\u95f4\u5206\u76f8\uff0c\u8fd8\u628aread haplotagging\u653e\u8fdb\u5185\u5b58\uff0c\u51cf\u5c11\u4e34\u65f6BAM\u843d\u76d8\u3002\u8bba\u6587\u6307\u51fa\uff0c\u7ea670%\u7684pileup\u5019\u9009\u4f1a\u8fdb\u5165\u9488\u5bf9\u4f4e\u7f6e\u4fe1\u4f4d\u70b9\u7684haplotagging\u8def\u5f84\u3002<\/p>\n

\u8fd9\u610f\u5473\u7740\u74f6\u9888\u5206\u6563\u5728\u56db\u5904\uff1aCPU\u8d1f\u8d23\u5207\u5757\u548c\u7279\u5f81\u751f\u6210\uff0cGPU\u8d1f\u8d23\u795e\u7ecf\u7f51\u7edc\u63a8\u7406\uff0c\u5185\u5b58\u627f\u63a5\u5e76\u884c\u8fdb\u7a0b\u4e0ehaplotagging\uff0cNVMe\u8d1f\u8d23\u8bfb\u53d6\u5927BAM\u548c\u5199\u4e2d\u95f4\u7ed3\u679c\u3002\u8bba\u6587\u73af\u5883\u4e3a\u4e24\u989712\u6838Xeon Silver 4116\u548cRTX 4090\uff1b\u82e5\u670d\u52a1\u5668\u53ea\u67098\u4e2aCPU\u7ebf\u7a0b\uff0c\u6216BAM\u653e\u5728\u62e5\u6324\u7684\u7f51\u7edc\u76d8\uff0c\u663e\u5361\u518d\u5feb\u4e5f\u53ef\u80fd\u5403\u4e0d\u6ee1\u3002<\/p>\n

\u5f53\u524dv2\u53ef\u6267\u884c\u90e8\u7f72\uff1a\u5148\u9501\u955c\u50cf\u548c\u6a21\u578b<\/h2>\n

\u5b98\u65b9GPU\u955c\u50cf\u8981\u6c42Linux NVIDIA\u9a71\u52a8\u81f3\u5c11530.30.02\uff0c\u5e76\u5b89\u88c5NVIDIA Container Toolkit\u3002\u4e0b\u9762\u547d\u4ee4\u4f7f\u7528\u5f53\u524dPyTorch\u4e3b\u7ebf\uff0c\u8f93\u5165\u76ee\u5f55\u5fc5\u987b\u4f7f\u7528\u7edd\u5bf9\u8def\u5f84\uff1a<\/p>\n

INPUT_DIR=\/data\/clair3\/input\r\nOUTPUT_DIR=\/data\/clair3\/output\r\nTHREADS=32\r\nMODEL_NAME=r1041_e82_400bps_sup_v520\r\n\r\ndocker run --rm --gpus '"device=0"' \\\r\n  -v ${INPUT_DIR}:${INPUT_DIR}:ro \\\r\n  -v ${OUTPUT_DIR}:${OUTPUT_DIR} \\\r\n  hkubal\/clair3:gpu \\\r\n  \/opt\/bin\/run_clair3.sh \\\r\n  --bam_fn=${INPUT_DIR}\/sample.bam \\\r\n  --ref_fn=${INPUT_DIR}\/GRCh38.fa \\\r\n  --threads=${THREADS} --platform=ont \\\r\n  --model_path=\/opt\/models\/${MODEL_NAME} \\\r\n  --output=${OUTPUT_DIR} --use_gpu \\\r\n  --remove_intermediate_dir\r\n<\/code><\/pre>\n
\u8fd0\u884c\u524d\u68c0\u67e5BAM\u5df2\u6309\u5750\u6807\u6392\u5e8f\u5e76\u5efa\u7acb\u7d22\u5f15\uff0cFASTA\u53ca\u5176\u7d22\u5f15\u4e0e\u6bd4\u5bf9\u53c2\u8003\u5b8c\u5168\u4e00\u81f4\u3002ONT\u6a21\u578b\u5fc5\u987b\u5339\u914d\u5b54\u578b\u3001\u5316\u5b66\u7248\u672c\u3001basecaller\u4e0eHAC\/SUP\u6a21\u5f0f\u3002\u5f53\u524d\u4ed3\u5e93\u5bf9R10.4.1 E8.2\u5217\u51fa\u4e86Dorado v6.0.0 HAC\u3001v5.2.0 SUP\u7b49\u6a21\u578b\uff1b\u82e5BAM\u542bDorado mv<\/code>\u6807\u7b7e\u5e76\u9009\u62e9with_mv<\/code>\u6a21\u578b\uff0c\u8fd8\u5fc5\u987b\u542f\u7528--enable_dwell_time<\/code>\u3002\u6ca1\u6709move table\u65f6\u4e0d\u8981\u5f3a\u884c\u4f7f\u7528\u4fe1\u53f7\u611f\u77e5\u6a21\u578b\u3002<\/p>\n
\u5148\u7528\u4e00\u6761\u67d3\u8272\u4f53\u505a\u201c\u8d44\u6e90\u4f53\u68c0\u201d<\/h2>\n
\u6b63\u5f0f\u5168\u57fa\u56e0\u7ec4\u524d\uff0c\u53ef\u52a0--ctg_name=chr20<\/code>\u505a\u4ee3\u8868\u6027\u8bd5\u8dd1\uff0c\u540c\u65f6\u8bb0\u5f55nvidia-smi dmon<\/code>\u3001\/usr\/bin\/time -v<\/code>\u548c\u78c1\u76d8\u541e\u5410\u3002\u81f3\u5c11\u4fdd\u5b58GPU\u5cf0\u503c\u3001\u5e73\u5747\u5229\u7528\u7387\u3001\u7cfb\u7edf\u5185\u5b58\u3001\u5899\u949f\u65f6\u95f4\u3001\u8f93\u5165BAM\u5927\u5c0f\u3001\u8986\u76d6\u5ea6\u4e0e\u6700\u7ec8VCF\u4f4d\u70b9\u6570\u3002GPU\u5229\u7528\u7387\u4f4e\u4e14CPU\u6ee1\u8f7d\uff0c\u5148\u589e\u52a0\u7ebf\u7a0b\u6216\u8c03\u6574\u5e76\u53d1\uff1bI\/O\u7b49\u5f85\u9ad8\uff0c\u5148\u628aBAM\u548c\u8f93\u51fa\u653e\u5230\u672c\u5730NVMe\uff1b\u663e\u5b58\u4e0d\u8db3\uff0c\u518d\u8003\u8651\u66f4\u6362GPU\u6216\u964d\u4f4e\u5e76\u884c\u538b\u529b\u3002<\/p>\n
\u5b98\u65b9\u9ed8\u8ba4--chunk_size<\/code>\u4e3a500\u4e07\u78b1\u57fa\u3002\u5757\u592a\u5927\uff0c\u5e76\u884c\u4efb\u52a1\u4e0d\u591f\uff1b\u5757\u592a\u5c0f\uff0c\u53c8\u4f1a\u589e\u52a0\u8c03\u5ea6\u548cI\/O\u5f00\u9500\u3002\u4e0d\u8981\u53ea\u8ffd\u6c42\u6700\u77ed\u5355\u6837\u672c\u65f6\u95f4\uff1a\u6279\u91cf\u961f\u5217\u4e2d\uff0c\u4e00\u5f20GPU\u914d\u591a\u4e2a\u6837\u672c\u53ef\u80fd\u53d1\u751f\u663e\u5b58\u4e89\u7528\uff0c\u800c32\u7ebf\u7a0b\u4efb\u52a1\u5e76\u53d1\u4e5f\u4f1a\u8fc5\u901f\u8017\u5c3dCPU\u3002\u66f4\u7a33\u59a5\u7684\u7b56\u7565\u662f\u5148\u6d4b\u5355\u6837\u672c\u8d44\u6e90\u66f2\u7ebf\uff0c\u518d\u51b3\u5b9a\u6bcf\u8282\u70b9\u5e76\u53d1\u6570\uff0c\u5e76\u4e3a\u5931\u8d25\u91cd\u8dd1\u4fdd\u7559\u72ec\u7acb\u8f93\u51fa\u76ee\u5f55\u548c\u5b8c\u6574\u65e5\u5fd7\u3002<\/p>\n
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