{"id":70105,"date":"2026-11-14T23:10:49","date_gmt":"2026-11-14T15:10:49","guid":{"rendered":"https:\/\/www.biocloudservice.com\/wordpress\/?p=70105"},"modified":"2026-11-14T23:10:49","modified_gmt":"2026-11-14T15:10:49","slug":"gatk-gvcf-reference-blocks-zero-depth-genotype","status":"publish","type":"post","link":"https:\/\/www.biocloudservice.com\/wordpress\/gatk-gvcf-reference-blocks-zero-depth-genotype\/","title":{"rendered":"GATK \u5b9e\u8dd1\uff5cgVCF \u91cc\u7684 0\/0\uff0c\u6709\u65f6\u56db\u5341\u6761\u8bfb\u6bb5\u652f\u6301\uff0c\u6709\u65f6\u4e00\u6761\u4e5f\u6ca1\u6709"},"content":{"rendered":"
\n

\u590d\u6838\u961f\u5217\u91cc\u7684\u67d0\u4e2a\u4f4d\u70b9\u65f6\uff0c\u5e38\u6709\u4eba\u4ece\u666e\u901a VCF \u627e\u4e0d\u5230\u8bb0\u5f55\uff0c\u63a5\u7740\u95ee\u201c\u8fd9\u4e2a\u4eba\u662f\u4e0d\u662f\u53c2\u8003\u7eaf\u5408\u201d\u3002\u628a\u540c\u4e00\u4e2a\u4eba\u7684 gVCF \u6253\u5f00\uff0c\u6709\u65f6\u80fd\u770b\u89c1\u53c2\u8003\u57fa\u56e0\u578b\uff0c\u4f46\u4e5f\u53ef\u80fd\u540c\u65f6\u770b\u5230\u6df1\u5ea6\u4e3a\u96f6\u3002\u6211\u4eec\u7ed9 GATK \u4e00\u6bb5\u786e\u5b9a\u6709\u56db\u5341\u6761\u8bfb\u6bb5\u7684\u533a\u57df\u3001\u4e00\u4e2a\u4eba\u5de5\u6742\u5408\u4f4d\u70b9\u548c\u4e00\u6bb5\u5b8c\u5168\u6ca1\u6709\u8bfb\u6bb5\u7684\u533a\u57df\uff0c\u8ba9\u5b83\u5206\u522b\u8f93\u51fa\u9010\u78b1\u57fa\u548c\u5206\u5757\u7684 gVCF\uff0c\u518d\u8fd0\u884c\u57fa\u56e0\u5206\u578b\u3002\u76f8\u540c\u8f93\u5165\u5f97\u5230\u4e86\u56db\u767e\u96f6\u4e00\u884c\u3001\u56db\u5341\u884c\u548c\u4e00\u884c\u3002\u6311\u51fa\u5176\u4e2d\u56db\u4e2a\u4f4d\u7f6e\uff0c\u5c31\u80fd\u533a\u5206\u6587\u4ef6\u538b\u7f29\u3001\u53c2\u8003\u8bc1\u636e\u4e0d\u8db3\u548c\u538b\u6839\u6ca1\u5206\u6790\u8fc7\u8fd9\u4e09\u79cd\u60c5\u5f62\u3002<\/p>\n

\u4e00\u6761\u53c2\u8003\u5757\u4ee3\u8868\u54ea\u4e2a\u8303\u56f4<\/h2>\n

HaplotypeCaller \u7684\u53c2\u8003\u7f6e\u4fe1\u5ea6\u6a21\u5f0f\u65e2\u4fdd\u7559\u5177\u4f53\u53d8\u5f02\u5019\u9009\uff0c\u4e5f\u4e3a\u5176\u4f59\u4f4d\u7f6e\u8bb0\u5f55\u76f8\u5bf9\u4e8e\u53c2\u8003\u7b49\u4f4d\u7684\u8bc1\u636e\u3002\u5728\u9010\u78b1\u57fa\u6a21\u5f0f\u4e2d\uff0c\u6bcf\u4e2a\u4f4d\u70b9\u5355\u72ec\u5360\u884c\u3002\u5728\u5206\u5757\u6a21\u5f0f\u4e2d\uff0c\u76f8\u90bb\u4e14\u6ee1\u8db3\u5206\u7ec4\u6761\u4ef6\u7684\u975e\u53d8\u5f02\u4f4d\u7f6e\u53ef\u4ee5\u538b\u6210\u4e00\u6761\u5e26\u7ed3\u675f\u5750\u6807\u7684\u8bb0\u5f55\u3002\u68c0\u7d22\u67d0\u4e2a\u4f4d\u7f6e\u65f6\uff0c\u8981\u5224\u65ad\u5b83\u662f\u5426\u5904\u5728\u4e00\u6761\u8bb0\u5f55\u8986\u76d6\u7684\u533a\u95f4\uff0c\u800c\u4e0d\u80fd\u53ea\u67e5\u8d77\u70b9\u7b49\u4e8e\u8be5\u4f4d\u7f6e\u7684\u884c\u3002\u5e26\u5c16\u62ec\u53f7\u7684\u975e\u53c2\u8003\u5360\u4f4d\u7b26\u8868\u793a\u6a21\u578b\u4e3a\u672a\u663e\u5f0f\u5217\u51fa\u7684\u66ff\u4ee3\u7b49\u4f4d\u9884\u7559\u53ef\u80fd\u6027\uff0c\u65e0\u6cd5\u636e\u6b64\u65ad\u8a00\u6837\u672c\u5728\u8be5\u4f4d\u7f6e\u5e26\u6709\u4e00\u4e2a\u65b0\u7684\u7b49\u4f4d\u3002GATK \u7684\u53c2\u8003\u7f6e\u4fe1\u5ea6\u6a21\u578b\u8bf4\u660e<\/a><\/p>\n

\u5206\u5757\u65f6\u8fd8\u8981\u533a\u5206\u8be5\u5757\u7684\u6c47\u603b\u6df1\u5ea6\u548c\u6700\u4f4e\u6df1\u5ea6\u3002\u524d\u8005\u53ef\u4ee5\u5e2e\u52a9\u4e86\u89e3\u8be5\u533a\u95f4\u5178\u578b\u7684\u8bc1\u636e\u91cf\uff0c\u540e\u8005\u63d0\u793a\u5757\u5185\u8f83\u5f31\u5904\u7684\u6df1\u5ea6\u3002\u9700\u8981\u77e5\u9053\u4e00\u4e2a\u5177\u4f53\u78b1\u57fa\u5230\u5e95\u6709\u51e0\u6761\u53ef\u7528\u89c2\u6d4b\uff0c\u5e94\u56de\u5230\u9010\u78b1\u57fa\u8f93\u51fa\u53ca\u76f8\u5e94\u7684\u6bd4\u5bf9\u8bc1\u636e\u3002\u5373\u4f7f\u5bf9\u76f8\u540c\u6587\u4ef6\u8fd0\u884c\u53e6\u4e00\u4e2a\u6df1\u5ea6\u547d\u4ee4\uff0c\u4e0d\u540c\u7684\u8d28\u91cf\u3001\u91cd\u590d\u3001\u914d\u5bf9\u91cd\u53e0\u5904\u7406\u4e5f\u53ef\u80fd\u4ea7\u751f\u4e0d\u540c\u8ba1\u6570\uff0c\u6838\u5bf9\u65f6\u8981\u8bb0\u5f55\u91c7\u7528\u7684\u6761\u4ef6\u3002GATK \u5bf9 GVCF \u5b57\u6bb5\u548c\u53c2\u8003\u5757\u7684\u89e3\u91ca<\/a><\/p>\n

\u5b9e\u8dd1\u7ecf\u9a8c\uff5c\u5728\u540c\u4e00\u6bb5\u53c2\u8003\u4e0a\u540c\u65f6\u5236\u9020\u56db\u79cd\u60c5\u51b5<\/h2>\n

\u6211\u4eec\u5b89\u88c5 GATK 4.7.0.0\uff0c\u5728\u4e24\u5343\u78b1\u57fa\u7684\u4eba\u9020\u53c2\u8003\u4e0a\u6784\u9020\u56db\u5341\u6761\u957f\u5ea6\u4e3a\u4e00\u767e\u7684\u5355\u7aef\u6bd4\u5bf9\u3002\u5b83\u4eec\u8d77\u70b9\u9519\u5f00\uff0c\u5171\u540c\u8986\u76d6\u7b2c\u56db\u767e\u4e94\u5341\u4f4d\u3002\u4e8c\u5341\u6761\u643a\u5e26\u53c2\u8003 G\uff0c\u4e8c\u5341\u6761\u643a\u5e26\u66ff\u4ee3 A\uff0c\u4e24\u4e2a\u7b49\u4f4d\u5404\u81ea\u90fd\u5b89\u6392\u4e86\u6b63\u53cd\u94fe\u89c2\u6d4b\u3002\u7ed9\u6587\u4ef6\u8865\u4e0a\u8bfb\u7ec4\u548c\u6837\u672c\uff0c\u6392\u5e8f\u5efa\u7d22\u5f15\uff0c\u540c\u65f6\u4e3a\u53c2\u8003\u5efa\u7d22\u5f15\u548c\u5b57\u5178\u3002\u968f\u540e\u53ea\u8bf7\u6c42\u7b2c\u4e09\u767e\u81f3\u7b2c\u4e03\u767e\u4f4d\uff0c\u4e24\u7aef\u90fd\u8ba1\u5165\uff0c\u5171\u56db\u767e\u96f6\u4e00\u4e2a\u78b1\u57fa\u3002\u6240\u6709\u7ed3\u679c\u6765\u81ea\u8fd9\u4e00\u4efd BAM\uff0c\u4e0b\u9762\u5404\u5217\u53ef\u4ee5\u6309\u5750\u6807\u76f4\u63a5\u590d\u6838\u3002<\/p>\n

\n\n\n\n\n\n\n\n\n
\u4f4d\u7f6e<\/th>\n\u5206\u5757 gVCF \u91cc\u627e\u5230\u4ec0\u4e48<\/th>\n\u9010\u78b1\u57fa\u6216\u6700\u7ec8\u7ed3\u679c<\/th>\n<\/tr>\n<\/thead>\n
325\uff0c\u65e0\u8986\u76d6<\/td>\n300\u2013381 \u5757\uff0cGT 0\/0\uff0cGQ 0\uff0cMIN_DP 0<\/td>\n\u9010\u78b1\u57fa DP 0<\/td>\n<\/tr>\n
426\uff0c\u6709\u8986\u76d6<\/td>\n409\u2013449 \u5757\uff0cGT 0\/0\uff0cGQ 99\uff0cMIN_DP 33<\/td>\n\u9010\u78b1\u57fa DP 40\uff0cAD 40,0<\/td>\n<\/tr>\n
450\uff0c\u690d\u5165 G\u2192A<\/td>\nGT 0\/1\uff0cAD 20,20,0<\/td>\n\u5206\u578b\u540e GT 0\/1\uff0cAD 20,20<\/td>\n<\/tr>\n
750\uff0c\u8bf7\u6c42\u8303\u56f4\u5916<\/td>\n\u627e\u4e0d\u5230\u8986\u76d6\u6b64\u5904\u7684\u8bb0\u5f55<\/td>\n\u4e24\u79cd gVCF \u5747\u65e0\u8be5\u4f4d\u7f6e<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<\/div>\n
\"\u540c\u662f
\u5bf9\u4e00\u4e2a\u5408\u6210\u6742\u5408\u4f4d\u70b9\u540c\u65f6\u8fd0\u884c\u5206\u5757\u3001\u9010\u78b1\u57fa\u53ca\u6700\u7ec8\u5206\u578b\u3002<\/figcaption><\/figure>\n

\u7b2c\u4e09\u767e\u4e8c\u5341\u4e94\u4f4d\u548c\u7b2c\u56db\u767e\u4e8c\u5341\u516d\u4f4d\u5728\u5206\u5757\u7ed3\u679c\u91cc\u90fd\u5199\u96f6\u659c\u7ebf\u96f6\u3002\u524d\u8005\u57fa\u56e0\u578b\u8d28\u91cf\u4e3a\u96f6\uff0c\u4e09\u79cd\u53ef\u80fd\u57fa\u56e0\u578b\u5bf9\u5e94\u7684\u4f3c\u7136\u503c\u90fd\u4e00\u6837\uff0c\u4e14\u6ca1\u6709\u6d4b\u5e8f\u6df1\u5ea6\u3002\u628a\u5b83\u5f53\u6210\u5df2\u53ef\u9760\u5224\u5230\u53c2\u8003\u57fa\u56e0\u578b\uff0c\u4f1a\u628a\u6ca1\u6709\u8bc1\u636e\u7684\u4eba\u52a0\u5165\u53ef\u5224\u5b9a\u5206\u6bcd\u3002\u540e\u8005\u7684\u9010\u78b1\u57fa\u8f93\u51fa\u5219\u786e\u5b9e\u6709\u56db\u5341\u6761\u53c2\u8003\u89c2\u6d4b\u3001\u96f6\u6761\u5176\u4ed6\u89c2\u6d4b\uff0c\u57fa\u56e0\u578b\u8d28\u91cf\u4e5d\u5341\u4e5d\u3002\u5b83\u6240\u5728\u7684\u53c2\u8003\u5757\u62a5\u544a\u6700\u4f4e\u6df1\u5ea6\u4e09\u5341\u4e09\uff0c\u8bf4\u660e\u4e0d\u80fd\u628a\u5f53\u524d\u4f4d\u70b9\u7684\u56db\u5341\u7167\u6284\u7ed9\u90a3\u4e00\u6574\u6bb5\u3002\u53f3\u8fb9\u672a\u8986\u76d6\u7684\u7b2c\u516d\u767e\u4e94\u5341\u4f4d\u4e5f\u80fd\u5728\u53e6\u4e00\u6761\u96f6\u8d28\u91cf\u53c2\u8003\u5757\u91cc\u627e\u5230\uff0c\u800c\u7b2c\u4e03\u767e\u4e94\u5341\u4f4d\u8fde\u5757\u90fd\u6ca1\u6709\uff0c\u4e24\u8005\u5728\u53ef\u89e3\u91ca\u8303\u56f4\u4e0a\u6709\u672c\u8d28\u5dee\u522b\u3002<\/p>\n

\u5207\u5230\u9010\u78b1\u57fa\u6a21\u5f0f\u5f97\u5230\u56db\u767e\u96f6\u4e00\u884c\uff0c\u628a\u5206\u5757\u6587\u4ef6\u7684\u8986\u76d6\u8de8\u5ea6\u6309\u4e00\u57fa\u95ed\u533a\u95f4\u7d2f\u52a0\uff0c\u540c\u6837\u8986\u76d6\u56db\u767e\u96f6\u4e00\u4e2a\u4f4d\u7f6e\uff0c\u53ea\u7528\u4e86\u56db\u5341\u884c\u3002\u5c06\u5206\u5757\u6587\u4ef6\u4ea4\u7ed9 GenotypeGVCFs\uff0c\u6309\u672c\u6b21\u9ed8\u8ba4\u8f93\u51fa\u5f97\u5230\u4e00\u6761\u4f4d\u4e8e\u7b2c\u56db\u767e\u4e94\u5341\u4f4d\u7684\u6742\u5408\u53d8\u5f02\u3002\u539f\u59cb\u7b49\u4f4d\u6df1\u5ea6\u5411\u91cf\u4e2d\u7b2c\u4e09\u4e2a\u96f6\u5bf9\u5e94\u975e\u53c2\u8003\u5360\u4f4d\u7b26\uff0c\u5206\u578b\u540e\u7684\u4e24\u9879\u6df1\u5ea6\u5206\u522b\u662f\u4e8c\u5341\u548c\u4e8c\u5341\u3002\u6700\u7ec8\u6587\u4ef6\u4e0d\u518d\u5217\u51fa\u7b2c\u4e09\u767e\u4e8c\u5341\u4e94\u4f4d\u6216\u7b2c\u56db\u767e\u4e8c\u5341\u516d\u4f4d\uff0c\u4f46\u5b83\u4eec\u5728\u8f93\u5165\u6837\u672c\u91cc\u7684\u53c2\u8003\u8bc1\u636e\u76f8\u5dee\u5f88\u5927\uff0c\u4e0d\u80fd\u4ece\u6700\u7ec8\u6587\u4ef6\u7684\u6c89\u9ed8\u53cd\u63a8\u51fa\u8bc1\u636e\u76f8\u7b49\u3002HaplotypeCaller \u5b98\u65b9\u5de5\u4f5c\u6d41\u7a0b<\/a><\/p>\n

gatk HaplotypeCaller -R ref.fa -I reads.bam -L chrToy:300-700 -ERC GVCF -O bands.g.vcf\r\ngatk HaplotypeCaller -R ref.fa -I reads.bam -L chrToy:300-700 -ERC BP_RESOLUTION -O bases.g.vcf\r\ngatk GenotypeGVCFs -R ref.fa -V bands.g.vcf -L chrToy:300-700 -O called.vcf\r\n<\/code><\/pre>\n
\u8fd8\u53ef\u4ee5\u505a\u4e00\u6b21\u4e0d\u4f9d\u8d56\u7279\u6b8a\u8f6f\u4ef6\u7684\u6838\u7b97\u3002\u8bfb\u53d6\u6bcf\u884c\u7684\u8d77\u70b9\uff0c\u82e5\u6709\u7ed3\u675f\u5b57\u6bb5\u5c31\u4f7f\u7528\u5b83\uff0c\u6ca1\u6709\u5219\u6309\u53c2\u8003\u7b49\u4f4d\u957f\u5ea6\u786e\u5b9a\u8986\u76d6\u8303\u56f4\u3002\u7528\u7ed3\u675f\u51cf\u53bb\u8d77\u70b9\u518d\u52a0\u4e00\uff0c\u9010\u884c\u7d2f\u8ba1\uff0c\u540c\u65f6\u68c0\u67e5\u76f8\u90bb\u8bb0\u5f55\u662f\u5426\u91cd\u53e0\u6216\u7559\u4e0b\u7a7a\u9699\u3002\u5982\u679c\u53ea\u7528\u884c\u6570\u5f53\u4f5c\u5904\u7406\u7684\u78b1\u57fa\u6570\uff0c\u4f1a\u628a\u672c\u6b21\u56db\u5341\u884c\u8bef\u62a5\u4e3a\u53ea\u5206\u6790\u4e86\u56db\u5341\u4e2a\u4f4d\u70b9\u3002\u5bf9\u4e8e\u5305\u542b\u8f83\u957f\u7f3a\u5931\u6216\u663e\u5f0f\u591a\u7b49\u4f4d\u7684\u771f\u5b9e\u7ed3\u679c\uff0c\u5148\u660e\u786e\u662f\u6838\u67e5\u53c2\u8003\u5757\u8986\u76d6\u8303\u56f4\uff0c\u8fd8\u662f\u7edf\u8ba1\u53d8\u5f02\u5f71\u54cd\u7684\u78b1\u57fa\uff0c\u4e0d\u5b9c\u8ba9\u540c\u4e00\u5957\u6c42\u548c\u540c\u65f6\u627f\u62c5\u4e24\u79cd\u4efb\u52a1\u3002<\/p>\n
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