{"id":70126,"date":"2026-11-14T23:24:43","date_gmt":"2026-11-14T15:24:43","guid":{"rendered":"https:\/\/www.biocloudservice.com\/wordpress\/?p=70126"},"modified":"2026-11-14T23:24:43","modified_gmt":"2026-11-14T15:24:43","slug":"deepvariant-small-model-cnn-wgs-variant-quality-na12878","status":"publish","type":"post","link":"https:\/\/www.biocloudservice.com\/wordpress\/deepvariant-small-model-cnn-wgs-variant-quality-na12878\/","title":{"rendered":"DeepVariant \u5b9e\u8dd1\uff5c\u5173\u95ed\u5c0f\u6a21\u578b\uff0cCNN \u8f93\u5165\u4ece 24 \u589e\u5230 84\uff0c\u4e3a\u4ec0\u4e48\u901a\u8fc7\u7684\u4ecd\u662f 72 \u4e2a\u4f4d\u70b9\uff1f"},"content":{"rendered":"
\n

DeepVariant \u7684\u65e5\u5fd7\u91cc\u4f1a\u540c\u65f6\u51fa\u73b0\u5019\u9009\u6570\u3001\u751f\u6210\u7684\u6837\u4f8b\u6570\u3001\u6a21\u578b\u9884\u6d4b\u6570\u548c\u6700\u7ec8 VCF \u884c\u6570\u3002\u53ea\u770b\u5377\u79ef\u7f51\u7edc\u5904\u7406\u4e86\u591a\u5c11\u4e2a\u56fe\u50cf\uff0c\u5f88\u5bb9\u6613\u8bef\u5224\u67d0\u6279\u6570\u636e\u6f0f\u6389\u4e86\u53d8\u5f02\u3002\u6211\u4eec\u5728\u516c\u5f00\u6837\u672c NA12878 \u7684\u4e8c\u5341\u53f7\u67d3\u8272\u4f53\u4e0a\uff0c\u5bf9\u540c\u4e00\u4e07\u4f59\u4e2a\u78b1\u57fa\u5b9e\u9645\u8dd1\u4e86\u4e24\u6b21 DeepVariant 1.10.0\u3002\u4e24\u6b21\u90fd\u4ece\u6bd4\u5bf9\u6587\u4ef6\u5f00\u59cb\uff0c\u7528\u540c\u4e00\u4e2a\u5168\u57fa\u56e0\u7ec4\u77ed\u8bfb\u957f\u6a21\u578b\u5b8c\u6574\u6267\u884c\u5230 VCF \u548c gVCF\u3002\u5173\u95ed\u5c0f\u6a21\u578b\u540e\uff0c\u5377\u79ef\u7f51\u7edc\u6536\u5230\u7684\u6837\u4f8b\u4ece\u4e8c\u5341\u56db\u589e\u5230\u516b\u5341\u56db\u3002\u4e24\u4efd\u901a\u8fc7\u8fc7\u6ee4\u7684\u7ed3\u679c\u5374\u6709\u5b8c\u5168\u76f8\u540c\u7684\u4e03\u5341\u4e8c\u4e2a\u53d8\u5f02\u952e\uff0c\u8fde\u57fa\u56e0\u578b\u4e5f\u4e00\u81f4\uff0c\u5176\u4e2d\u4e94\u5341\u56db\u4e2a\u7684\u57fa\u56e0\u578b\u8d28\u91cf\u53d1\u751f\u4e86\u53d8\u5316\u3002<\/p>\n

\u5148\u8ba4\u6e05\u4e24\u6761\u63a8\u65ad\u8def\u5f84<\/h2>\n

\u8fd9\u4e2a\u7248\u672c\u7684\u5168\u57fa\u56e0\u7ec4\u6d41\u7a0b\u4f1a\u5148\u68c0\u67e5\u5019\u9009\u3002\u5bf9\u9002\u7528\u7684\u53cc\u7b49\u4f4d\u5019\u9009\uff0c\u5c0f\u6a21\u578b\u8bfb\u53d6\u7b49\u4f4d\u652f\u6301\u3001\u8d28\u91cf\u548c\u9644\u8fd1\u4f4d\u7f6e\u7b49\u7279\u5f81\uff0c\u5982\u679c\u5f97\u5230\u8db3\u591f\u6709\u628a\u63e1\u7684\u5206\u7c7b\uff0c\u53ef\u4ee5\u76f4\u63a5\u628a\u9884\u6d4b\u4ea4\u7ed9\u540e\u5904\u7406\u3002\u9700\u8981\u66f4\u5b8c\u6574\u5224\u8bfb\u7684\u5019\u9009\u4f1a\u751f\u6210\u7f16\u7801\u8bfb\u6bb5\u5806\u53e0\u4fe1\u606f\u7684\u591a\u901a\u9053\u56fe\u50cf\uff0c\u518d\u4ea4\u7ed9\u5377\u79ef\u7f51\u7edc\u3002\u4e24\u6761\u8def\u5f84\u6700\u7ec8\u6c47\u5230\u540e\u5904\u7406\u9636\u6bb5\u3002\u56e0\u6b64\uff0c\u65e5\u5fd7\u91cc\u201c\u9001\u8fdb\u5377\u79ef\u7f51\u7edc\u201d\u7684\u6570\u76ee\u53ea\u63cf\u8ff0\u5176\u4e2d\u4e00\u8def\u3002\u540c\u4e00\u4e2a\u5019\u9009\u4f4d\u7f6e\u542b\u591a\u4e2a\u53ef\u8003\u8651\u7684\u7b49\u4f4d\u7ec4\u5408\u65f6\uff0c\u4f4d\u70b9\u6570\u4e0e\u56fe\u50cf\u6837\u4f8b\u6570\u4e5f\u53ef\u80fd\u4e0d\u540c\uff0c\u4e0d\u80fd\u9884\u8bbe\u4e00\u6761\u5019\u9009\u5fc5\u5b9a\u5bf9\u5e94\u4e00\u5f20\u56fe\u3002DeepVariant \u4f5c\u8005\u5bf9\u5c0f\u6a21\u578b\u53ca\u5176\u8f93\u5165\u7684\u8bf4\u660e<\/a><\/p>\n

\u8fd9\u91cc\u7684\u6a21\u578b\u7c7b\u578b\u8981\u4e0e\u6d4b\u5e8f\u65b9\u6cd5\u76f8\u7b26\u3002\u6211\u4eec\u91c7\u7528\u5b98\u65b9\u5feb\u901f\u5165\u95e8\u7684\u77ed\u8bfb\u957f\u6bd4\u5bf9\u7247\u6bb5\u548c\u5b83\u914d\u5957\u7684\u53c2\u8003\u6587\u4ef6\uff0c\u4fdd\u7559\u539f\u59cb\u67d3\u8272\u4f53\u540d\u79f0\u4e0e\u7d22\u5f15\u3002\u7b2c\u4e00\u6b21\u4f7f\u7528\u9ed8\u8ba4\u914d\u7f6e\uff0c\u7b2c\u4e8c\u6b21\u53ea\u589e\u52a0\u5173\u95ed\u5c0f\u6a21\u578b\u7684\u53c2\u6570\uff0c\u4e24\u6b21\u90fd\u53ea\u7528\u4e00\u4e2a\u5206\u7247\uff0c\u7ed3\u679c\u5199\u5165\u4e0d\u540c\u76ee\u5f55\u3002\u8fd9\u4e00\u5bf9\u7167\u5904\u7406\u7684\u662f\u540c\u4e00\u53c2\u8003\u533a\u95f4\u5185\u7684\u6a21\u578b\u5206\u5de5\u548c\u8f93\u51fa\u5dee\u5f02\u3002\u5b83\u6ca1\u6709\u8bad\u7ec3\u6a21\u578b\uff0c\u4e5f\u6ca1\u6709\u5728\u5168\u57fa\u56e0\u7ec4\u4f30\u7b97\u8017\u65f6\u6216\u6bd4\u8f83\u786c\u4ef6\u541e\u5410\u3002\u5b98\u65b9\u5feb\u901f\u5165\u95e8\u7684\u6570\u636e\u548c\u533a\u95f4<\/a><\/p>\n

\u5b9e\u8dd1\u7ecf\u9a8c\uff5c\u4ece\u4e24\u4efd\u65e5\u5fd7\u5bf9\u5230\u6700\u7ec8\u8fc7\u6ee4\u72b6\u6001<\/h2>\n

\u6211\u4eec\u5728 CPU \u4e0a\u8fd0\u884c\u4e86\u5b98\u65b9 1.10.0 \u955c\u50cf\u5185\u7684\u5b9e\u9645\u7a0b\u5e8f\u548c\u968f\u9644\u6743\u91cd\u3002\u8bf7\u6c42\u5750\u6807\u4e3a\u4e8c\u5341\u53f7\u67d3\u8272\u4f53\u7b2c\u4e00\u5343\u4e07\u81f3\u7b2c\u4e00\u5343\u96f6\u4e00\u4e07\u4f4d\uff0c\u6309\u4e00\u57fa\u95ed\u533a\u95f4\u5171\u4e00\u4e07\u96f6\u4e00\u4e2a\u78b1\u57fa\u3002\u4e24\u6b21\u90fd\u4ece\u76f8\u540c\u8f93\u5165\u53d1\u73b0\u4e03\u5341\u516b\u4e2a\u5019\u9009\u3002\u9ed8\u8ba4\u6d41\u7a0b\u62a5\u544a\u5c0f\u6a21\u578b\u5904\u7406\u5e76\u63a5\u53d7\u516d\u5341\u4e2a\u6837\u4f8b\uff0c\u53e6\u5199\u51fa\u4e8c\u5341\u56db\u4e2a\u4f9b\u5377\u79ef\u7f51\u7edc\u9884\u6d4b\u3002\u5173\u95ed\u5c0f\u6a21\u578b\u540e\uff0c\u5377\u79ef\u7f51\u7edc\u5b9e\u9645\u9884\u6d4b\u516b\u5341\u56db\u4e2a\uff0c\u4e24\u6b21\u540e\u5904\u7406\u65e5\u5fd7\u90fd\u8bb0\u5f55\u5904\u7406\u516b\u5341\u56db\u9879\u3002\u8fd9\u4e2a\u9636\u6bb5\u7684\u6837\u4f8b\u8ba1\u6570\u4e0e\u6700\u7ec8\u4f4d\u70b9\u884c\u6570\u6709\u4e0d\u540c\u7684\u7edf\u8ba1\u5355\u4f4d\u3002<\/p>\n

\n\n\n\n\n\n\n\n\n
\u540c\u4e00\u8f93\u5165\u7684\u5b9e\u9645\u8bfb\u6570<\/th>\n\u9ed8\u8ba4\u542f\u7528\u5c0f\u6a21\u578b<\/th>\n\u5173\u95ed\u5c0f\u6a21\u578b<\/th>\n<\/tr>\n<\/thead>\n
\u5019\u9009\uff0f\u9001\u5165 CNN \u7684\u6837\u4f8b<\/td>\n78\uff0f24<\/td>\n78\uff0f84<\/td>\n<\/tr>\n
VCF \u7684\u8bb0\u5f55\u6570<\/td>\n78<\/td>\n78<\/td>\n<\/tr>\n
PASS\uff0fRefCall\uff0fNoCall<\/td>\n72\uff0f6\uff0f0<\/td>\n72\uff0f5\uff0f1<\/td>\n<\/tr>\n
\u914d\u5957 gVCF \u7684\u8bb0\u5f55\u6570<\/td>\n228<\/td>\n228<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<\/div>\n
\"CNN
\u5bf9 NA12878 \u540c\u4e00\u6bb5\u77ed\u8bfb\u957f\u6570\u636e\u8fd0\u884c\u4e24\u6b21\u5b8c\u6574 WGS \u63a8\u65ad\u3002<\/figcaption><\/figure>\n

\u9ed8\u8ba4\u8f93\u51fa\u5e26\u6709\u6a21\u578b\u6765\u6e90\u5b57\u6bb5\uff0c\u4e03\u5341\u4e8c\u6761\u901a\u8fc7\u8bb0\u5f55\u4e2d\uff0c\u4e94\u5341\u4e94\u6761\u6765\u81ea\u5c0f\u6a21\u578b\uff0c\u5341\u4e03\u6761\u6765\u81ea\u5e38\u89c4\u5377\u79ef\u7f51\u7edc\u3002\u628a\u8fd9\u4e2a\u6570\u5b57\u548c\u65e5\u5fd7\u5bf9\u7167\uff0c\u5c0f\u6a21\u578b\u4e00\u5171\u63a5\u53d7\u4e86\u516d\u5341\u4e2a\u6837\u4f8b\uff0c\u5176\u4e2d\u5e76\u975e\u6bcf\u4e2a\u90fd\u6210\u4e86\u901a\u8fc7\u8fc7\u6ee4\u7684\u66ff\u4ee3\u53d8\u5f02\u3002\u5173\u95ed\u5c0f\u6a21\u578b\u540e\u7684 VCF \u6ca1\u6709\u9010\u6837\u672c\u7684\u8be5\u6765\u6e90\u5b57\u6bb5\uff0c\u6b64\u65f6\u5e94\u7ed3\u5408\u6267\u884c\u65e5\u5fd7\u8bb0\u5f55\u6a21\u5f0f\uff0c\u76f4\u63a5\u7b5b\u9009\u5c0f\u6a21\u578b\u6807\u7b7e\u4f1a\u628a\u8fd9\u4e2a\u6587\u4ef6\u7684\u8bb0\u5f55\u90fd\u6f0f\u6389\u3002\u60f3\u590d\u67e5\u8ba1\u6570\uff0c\u5148\u6309\u8fc7\u6ee4\u72b6\u6001\u5206\u7ec4\uff0c\u518d\u5728\u540c\u4e00\u7ec4\u5185\u7edf\u8ba1\u6765\u6e90\uff0c\u66f4\u5bb9\u6613\u4e0e\u6700\u7ec8\u7528\u4e8e\u4e0b\u6e38\u7684\u6e05\u5355\u6838\u5bf9\u3002<\/p>\n

\u540c\u4e00\u4f4d\u7f6e\u7684\u8bc1\u636e\u8fd8\u53ef\u4ee5\u9010\u9879\u590d\u67e5\u3002\u53d6\u968f\u4f8b\u9ad8\u7f6e\u4fe1\u533a\u95f4\u5185\u7684 chr20:10009227<\/code> \u4f5c\u5bf9\u7167\u3002\u53c2\u8003 A\u3001\u66ff\u4ee3 G\uff0c\u4e24\u6b21\u90fd\u62a5\u544a\u6742\u5408\uff0c\u6df1\u5ea6\u516d\u5341\u516d\uff0c\u7b49\u4f4d\u6df1\u5ea6\u4e09\u5341\u56db\u4e0e\u4e09\u5341\u4e8c\u3002\u9ed8\u8ba4\u5c0f\u6a21\u578b\u7ed9\u57fa\u56e0\u578b\u8d28\u91cf\u4e09\u5341\u56db\uff0c\u5173\u95ed\u540e\u5377\u79ef\u7f51\u7edc\u7ed9\u5341\u516d\u3002\u82e5\u62a5\u544a\u8981\u6c42\u57fa\u56e0\u578b\u8d28\u91cf\u81f3\u5c11\u4e8c\u5341\uff0c\u8fd9\u4e2a\u4f4d\u7f6e\u53ef\u4ee5\u5728\u4e24\u4efd\u539f\u59cb\u6587\u4ef6\u91cc\u90fd\u6807\u4e3a\u901a\u8fc7\uff0c\u6700\u540e\u5374\u56e0\u989d\u5916\u8fc7\u6ee4\u5f97\u5230\u4e24\u4e2a\u4e0d\u540c\u7684\u7ed3\u8bba\u3002\u4e03\u5341\u4e8c\u4e2a\u5171\u540c\u901a\u8fc7\u7684\u952e\u4e2d\uff0c\u6df1\u5ea6\u4e0e\u7b49\u4f4d\u6df1\u5ea6\u9010\u9879\u90fd\u4e00\u81f4\uff0c\u6b63\u597d\u628a\u8f93\u5165\u8bc1\u636e\u53d8\u5316\u4e0e\u8bc4\u5206\u53d8\u5316\u533a\u5206\u5f00\u3002<\/p>\n

# \u4ee5\u4e0b\u53c2\u6570\u52a0\u5230\u5b98\u65b9\u5feb\u901f\u5165\u95e8\u7684\u540c\u4e00\u4efd WGS \u547d\u4ee4\u4e2d\uff0c\u5206\u522b\u5199\u5165\u4e24\u4e2a\u76ee\u5f55\r\n# \u7b2c\u4e8c\u6b21\u8fd0\u884c\u589e\u52a0 --disable_small_model=true\r\nbcftools query -f '%CHROM\\t%POS\\t%REF\\t%ALT\\t%FILTER[\\t%GT:%GQ:%DP:%AD]\\n' output.vcf.gz\r\nbcftools view -f PASS -H output.vcf.gz | wc -l\r\n<\/code><\/pre>\n
\u4e3a\u4ec0\u4e48\u4e03\u5341\u4e8c\u6761\u76f8\u540c\u4e5f\u4e0d\u80fd\u7528\u6765\u5ba3\u5e03\u51c6\u786e\u7387\u76f8\u540c<\/h2>\n
\u8fd8\u6709\u4e00\u5904\u4f4d\u7f6e chr20:10009877<\/code>\uff0c\u4e24\u6b21\u8f93\u5165\u8bc1\u636e\u5747\u4e3a\u4e09\u5341\u4e09\u6761\u53c2\u8003\u548c\u4e94\u6761\u66ff\u4ee3\uff0c\u6837\u672c\u6df1\u5ea6\u4e09\u5341\u516b\u3002\u9ed8\u8ba4\u8f93\u51fa\u53c2\u8003\u578b\uff0c\u8fc7\u6ee4\u72b6\u6001\u4e3a\u53c2\u8003\u5224\u5b9a\uff0c\u5173\u95ed\u5c0f\u6a21\u578b\u540e\u8f93\u51fa\u7f3a\u5931\u57fa\u56e0\u578b\u3001\u72b6\u6001\u4e3a\u65e0\u6cd5\u8c03\u7528\u3002\u5b83\u4e0d\u5728\u90a3\u4e03\u5341\u4e8c\u6761\u901a\u8fc7\u6e05\u5355\u91cc\uff0c\u82e5\u53ea\u5bf9\u6bd4\u901a\u8fc7\u8bb0\u5f55\uff0c\u5c31\u770b\u4e0d\u5230\u8fd9\u4e2a\u5dee\u5f02\u3002\u8be5\u4f4d\u7f6e\u4e5f\u5728\u672c\u793a\u4f8b\u63d0\u4f9b\u7684\u9ad8\u7f6e\u4fe1\u8bc4\u4f30\u533a\u95f4\u4e4b\u5916\u3002\u4e0d\u80fd\u56e0\u4e3a\u793a\u4f8b\u771f\u503c\u8868\u6ca1\u6709\u5bf9\u5e94\u8bb0\u5f55\uff0c\u5c31\u65ad\u8a00\u5176\u4e2d\u4e00\u4e2a\u6a21\u578b\u5728\u8fd9\u91cc\u5224\u9519\u3002<\/p>\n
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